In order to guarantee the radar data communication in the air traffic control system, a new HDLC protocol controller based on the FPGA parallel technology was presented. In terms of the HDLC frame structure and the theory of cyclic redundancy check,the implementation of the modules, constructing and deconstructing HDLC protocol frame, producing and checking the CRC code, and adopting the FPGA new technology were discussed. A new parallel high level data link controller (HDLC) was designed using the hardware description language on the FPGA device. The HDLC protocol controller can construct or deconstruct the multi-channel HDLC protocol frames in parallel way. As a result, it improved the robust and reliability of the whole system.