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. The electronic design of quantum key distribution (QKD) control system based was presented 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 very-high-speed integrated circuits hardware description language (VHDL). The design was applied in the 1 km QKD distribution experiment during daytime, and its final key rate was greater than 1.5 kbps.