In order to put the CAN (Controller Area Network) into UHS (Unmanned Helicopter System) application, a universal CAN application layer protocol was developed. The problems which are data definition, telemetry, telecontrol data link bandwidth and so on in the CANaerospace V1.7 protocol application in UHS were improved. Redefining of the basic message format and the data identifier, the CANauh protocol for UHS was put forward. In order to verify the CANauh protocol, a proposal of UHS avionics system based on CAN data bus was chosen as the research object, the data on the CAN bus, data identifier distribution and bus schedule were designed and simulated by the CANoe tool. The CAN bus load on 10 ms basic period is 40.83%, data extended definition space is 67.4%, the duty factor of telemetry and telecontrol data link bandwidth is 66.7%, satisfying the requirements of UHS. The CANauh protocol will promote the CAN data bus application in new UHS, can avoid repeated design, increases the interoperability and reduces the cost of development and maintenance.