A method for updating factory default settings and boot loaders in an embedded system is disclosed. The method includes the steps of: recording factory default settings to each partition of a flash memory; installing the flash memory in the embedded system and doing function tests; generating a new boot loader comprising NVRAM variables; modifying a parameter of the NVRAM variables; and updating the new boot loader to the flash memory. The invention can be used to update boot loaders or a firmware, and generate new boot loaders based on documents modified by a user.