An apparatus and a method of controlling an information process system of a mobile apparatus using a flash memory. The information process system controlling the mobile apparatus has a main memory storing a user-set data and a flash memory storing a backup data of the user-set data stored in the main memory when a main power is turned off and/or when a backup command is input by a user. A programmed CPU controls the information process system by determining whether the main power is turned off and/or whether the backup command is input by the user, and backs up the main-memory user-set data to the flash memory. Accordingly, since the user-set data is backed-up to the flash memory when the main power is turned off, an initialization image and an initialization menu can be executed according to the user-set data when the mobile apparatus is re-operated.