Due to the high speed of data transmission in data acquisition system, the system need ensure the high speed data storage speed. This paper introduces a new bad block management of NAND Flash in a NAND Flash storage system, which is based on judging and jumping bad blocks by the unit of page. Compared with the traditional management by the unit of block, this design guarantees the speed of programming won’t decrease if bad blocks appear , improves the utilization rate of Flash storage resource, and decreases occupying the resource of cache. This design used in a high speed data acquisition system based on FPGA，test result shows that the bad block management makes sure the speed almost remain the same when bad blocks occur, and handles the NAND Flash bad block issues correctly with highly stability.