In order to capture and storage video data real-time for carrier-based photoelectric warning system, An acquisition and storage system based on FPGA is designed. To complete the asynchronous interface timing of the camera and the storage system, the video data which come from infrared camera and visible light camera is stored to FIFO by FPGA, and then four SDRAM as cache and ping-pong operation cache-data storage to the CF card, this structure not only takes advantage of high-speed reading and writing skills of CF card, but also to ensure the integrity of the video data. In the final experiment proved that the system can be effectively applied to ships the photoelectric warning scanning system, its performance fully meet the needs of practical application.