This paper presents a control problem of a twin rotor MIMO system (TRMS) based on the system on programmable chip (SoPC). The control system utilizes the cerebellar model articulation controller (CMAC) as a compensator for PID control. The CMAC has fast learning capability that can provide real time compensation for PID controller. In the hardware implementation, HCTL-2016 is used to encode AB phase voltage into digital signals. Verilog HDL is utilized to encode program that can receive and trigger signals from HCTL-2016 on Altera Nios II FPGA. By coding the programmable chip control signal can be passed to the controller. The processed signal is converted by a D/A converter and is transferred into voltage. The command signal is then sent back to the TRMS to control its movement. Experimental results show that the hybrid CMAC-PID can control the TRMS to reach desired position and track specified trajectory efficiently.