Aiming to the control of a tilt tri-rotor vertical take-off and landing (VTOL) aircraft, and the flight control system based on STM32 microprocessor was designed. Ten axes inertial navigation module was used to collect the real time position data and satellite navigation data of the carrier, and the attitude and location information was calculated by using fusion algorithm based on quaternion. Cascade PID control system was adopted, aiming at the real-time and high-accuracy feature of attitude control of UAV. Aiming at the unstable problem in the tilt tri-rotor VTOL aircraft, a PID controller with incomplete derivative was proposed. The controller adding a first-order inertial link in the derivative can reduce the negative effect of external interference on the system. Finally, the verify flight was carried out to test the pitch, yaw and roll motions of the aircraft. The results demonstrated that cascade PID controller with incomplete derivative can control the attitude of the tilt tri-rotor VTOL aircraft quickly, stably and accurately in helicopter mode, which had good robustness. In addition, cascade PID controller with incomplete derivative can reduce the difficulty of parameter tuning. The control system had a good performance with the setting of roll angle (inner ring Kp was 8.371, Kd was 3.015 and outer ring Kp was 5.1, Kd was 1.15), pitch angle (inner ring Kp was 3.137, Kd was 1.6 and outer ring Kp was 3.43, Ki was 0.003, Kd was 3.97), yaw angle (Kp was 9.30 and Ki was 0.11). And the controller designed could meet the performance requirements of the control system. It provided guidance for the follow-up study on flight control of the tilt tri-rotor VTOL aircraft. 