Abstract: With the booming development of quantum cryptography, the free-space quantum key distribution is an important research branch. It will play a critical role in the future global quantum communication. We presented the electronic design of QKD(Quantum Key Distribution) control system based on a Xilinx’s VirtexII-Pro series chip. extracting final quantum key and controlling peripheral circuit were implemented with the combination of the embedded hard core PowerPC405 in FPGA and the logic module designed by VHDL（Very-High-Speed Integrated Circuits Hardware Description Language）. The design has been applied in the 1 km QKD distribution experiment during the daytime, and its final key rate is greater than 1.5Kbps.