In order to achieve high-speed serial communication between the flight management module and the servo, booster, etc., a High-Level Data Link Control (HDLC) protocol controller based on Zynq-7000 All Programmable SoC (ZYNQ) was designed. The internal Programmable Logic (PL) and Processing System (PS) of ZYNQ exchange data through Advanced eXtensible Interface (AXI) bus and use dual First Input First Output (FIFO) for data caching; PL developed the control timing of HDLC communication protocol using Verilog language, and PS completed Cyclic Redundancy Check (CRC); Developed a synchronous half duplex RS485 bus interface schematic and printed circuit board with ZYNQ as the core. The actual application results show that the communication rate of the system can reach 4Mbit/s, and it operates stable and reliably without any errors, frame loss, and other phenomena.