How to Clone Hard Drive to Flash Drive (Bootable)

You can easily clone a hard drive to a flash drive while retaining its bootability with the help of the reliable disk cloning software - AOMEI Cloner.

By @Jonna
Last Updated August 1, 2025

Can I Copy My Entire Hard Drive to a Flash Drive?

 

I need to have a clone of my entire system drive on an external USB flash drive that I can use to:

RECOVER MY SYSTEM... if my hard drive dies for whatever reason, melts, or is stolen.

How can I do this?

Yes, you can copy the entire hard drive to a USB flash drive, but there are some things to keep in mind. A simple copy-paste operation will not work for a system drive that includes your operating system, boot files, hidden partitions, and system configurations. To truly copy everything, you need to do it via cloning. This ensures that system and recovery partitions, settings are migrated and preserved.

However, for this to work:

  • Your flash drive must have enough storage capacity to match or exceed the used space on the hard drive.
  • It must be formatted correctly, often in NTFS or exFAT, depending on your system.
  • You need a specialized disk cloning software that supports cloning hard drive to flash drive.

Best Cloning Software for Cloning Hard Drive to Flash Drive

Not all cloning tools support USB flash drives as destination targets, which makes choosing the right software critical. One standout option is AOMEI Cloner.

This software supports various drives, like HDD, SSD (SATA/NVMe, M.2), USB flash drive, SD card, etc. So you can use it to clone from HDD/SSD to USB flash drives, SD cards, as well as clone external hard drive to another external hard drive. Here are some features that make it ideal for cloning disk to USB drive:

AOMEI Cloner
Best System and Disk Cloning Software
  • Disk Clone - This copies one entire hard drive to another, including the operating system, applications, configurations, and settings, are transferred.
  • System Clone - This allows you to just move your operating system to another disk, leaving files not related to system startup behind.
  • Sector By Sector Clone - You can create an exact 1:1 replication of your hard drive to include all data and boot files.
  • Clone to Smaller Drive - It runs in Intelligent Clone by default to clone only the used space, supporting cloning from a large HDD to a smaller SSD or USB.
  • Bootable Media Creation - It is capable of creating bootable USB or CD/DVD, possible to clone hard drive with bootable USB.
Free Download
Win 11/10/8/7/Server
100% Secure

How to Clone Hard Drive to USB Flash Drive

To perform a disk clone to USB with bootable using AOMEI Cloner, follow these steps below.

Step 1: Prepare Your Devices

  • Backup important files on USB, as the cloning process will erase all data on it.
  • Make sure your flash drive has enough capacity (minimum 64GB for Windows OS).
  • Insert the USB flash drive into your computer. It is advised to use a USB 3.0 port for faster performance.

Step 2: Launch AOMEI Cloner for Disk Clone

Step 3: Select Source and Destination Drives

  • Source: Choose the hard drive you want to clone (usually "Disk 0").
  • Destination: Choose the USB flash drive.

Step 4: Enable Sector-by-Sector Clone (Optional)

Tick this option if you want to clone all sectors, including unused and bad ones. It guarantees a complete copy but requires more time and space.

Step 5: Start the Clone

Click Start Clone to clone hard drive to USB drive. The process may take several minutes to hours, depending on the size of your hard drive.

Benefits of Cloning Hard Drive to USB Drive

Cloning a hard drive to a USB flash drive has several advantages:

▶Create a Portable OS: It turns your flash drive into a bootable Live USB. Boot your system from anywhere, on any compatible machine.

▶Full system backup: It is like having a complete mirror of your system that you can revert to in emergencies. If your internal drive crashes, just boot from the USB.

▶Quick system restore: No need to reinstall Windows or configure software again. Just plug in the USB and you are back where you left off.v

▶Upgrade or replace hard drives: Clone your system to a USB, then clone back to a new internal SSD. A great workaround when upgrading hardware.

Summary

Whether you're preparing for the worst or just want a portable bootable system, using the right tool like AOMEI Cloner makes cloning hard drive to flash drive the process easy and foolproof. Also, you can run it as a USB drive clone tool, which makes cloning USB drive to SSD or HDD simple.

Free Download Windows 11/10/8/7/Server
Secure Download

FAQs on Cloning Hard Drive to Flash Drive

#1. How do I save everything on a computer to a flash drive?

To save all data from your computer, use a disk cloning tool like AOMEI Cloner. This ensures you're not just copying files, but cloning the entire structure - OS, programs, system files, hidden files, and boot records. Simply follow the cloning process mentioned above, selecting your internal hard drive as the source and the USB flash drive as the destination.

For a standard file copy (without OS), manually transfer folders to the flash drive, but remember- this method won't make your flash drive bootable.

#2. Is it better to clone or image a hard drive?

It depends on your purpose:

  • Cloning is best when you want an exact, ready-to-boot replica of your system on another drive- perfect for immediate use or quick recovery.
  • Imaging creates a compressed backup file (like a ZIP). It’s great for storage but needs restoration before use.

So, if you're aiming to boot from your flash drive, go with cloning. It offers instant usability with no restoration needed.

#3. What to do before cloning a hard drive?

Here is what you need to do:

  • Check flash drive size: Ensure it's large enough to hold your hard drive content.
  • Back up data: Just in case something goes wrong.
  • Clean up the drive: Delete unnecessary files to speed up cloning.
  • Defragment the source drive(optional): Helps the cloning tool operate efficiently.