A kind of watermelon seeds sorter system with linear CCD chip was designed based on the FPGA parallel computing platform. Through integrating CCD driver, dynamic image acquisition and processing algorithms, classification algorithm and valve control signal output in one FPGA chip, the hardware platform were designed. The color sorter prototype system had an output of 1.2～1.8 t/h, color sorting accuracy was 97.7%, ratio of color separation mass was 6~8. The good realtime and efficiency of the watermelon seeds sorter system based on FPGA were verified by the experiments that compared with the traditional industrial computer platform.