An autonomous control strategy is proposed and an embedded control system architecture platform is developed for a quadrotor unmanned aerial vehicle based on optical flow vision system. The self-motion estimation is obtained by fusing the optical flow data and data from the on-board inertial measurement unit, and then an inner-outer-loop proportion integration differentiation (PID) controller used the self-motion estimation as feedback signal. Unlike the traditional host-based control system architecture, the motion states are estimated through an onboard embedded computer and the control algorithm is operated through an onboard flight control board. Difficulty as the embedded control system architecture platform is, it is very useful for autonomous control flight. Experiment results are included to demonstrate the good performance of the proposed design.