A FPGA-based intelligent storage control system is provided that includes a FLASH main controller; a FLASH command former and an address generator with a memory function, for generating level signal of cross clock domain and automatically avoiding out-of-bounds writing. A configuration data former provides for driving and controlling a configuration writing in function by a writing configuration drive signal. An automatic reading configurator provides automatic configuration reading by internal drive signal to drive. A main data and auxiliary data former provides continuous storage of main data according to ping-pong operation for unequal width RAM operation. A FLASH data reading buffer and a multi-interface external drive module are also present. The system is applicable to an unmanned underwater vehicle and underwater acoustic equipment. The system and the application thereof, the problems of existing storage control systems during underwater working are solved, with the characteristics of reliability, simplicity or intelligence.