The invention discloses a remote upgrade method and system of a Squashfs read-only root file system. The remote update system comprises two mountable root file systems and a BOOT multi-boot control unit, wherein the two mountable root file systems include the Squashfs read-only root file system and a memory file system. The Squashfs read-only root file system and the memory file system correspond to a first device tree description file and a second device tree description file respectively, and the first device tree description file and the second device tree description file are used for identifying a storage area of the Squashfs read-only root file system to be read-only and readable and writable; the BOOT multi-boot control unit is used for analyzing different device tree description files by modifying boot marker bits and used for booting and analyzing the root file systems corresponding to the device tree description files; when the BOOT multi-boot control unit modifies the boot marker bits to be in an upgrade state, the second device tree description file is analyzed, the memory file system is mounted to serve as a root file system, and the Squashfs read-only root file system is remotely upgraded. By means of the remote upgrade method and system, maintainability and reliability of the system are enhanced on the basis that hardware cost is not increased, and meanwhile the problem that a remote area device maintenance system is high in maintenance cost and large in difficulty is solved.