In recent years, the positioning technology for unmanned aerial vehicle (UAV) has been developed rapidly. However, there are still challenges in terms of improving the computational efficiency, accuracy, and robustness of the algorithm for applications in fast flight with UAV. In this paper, we present a novel positioning system of UAV based on IMA-GPS (inertial measurement unit array -global positioning system) three-layer data fusion, which effectively solves the positioning problem of UAV. The first layer is the distributed filtering layer, the unscented Kalman filter serves as the local filter to process the measurements generated by each IMU in the IMA. The second layer is the IMA compensation fusion layer, the data of GPS is introduced to compensate for the deviation of the navigation results calculated by each IMU. The third layer is the GPS-IMA joint optimization layer, where the outputs of the IMA and GPS are fused to obtain the attitude, speed, and position. Simulation results show that the proposed method can realize an integrated navigation system which has low cost, high accuracy, and high computational speed, so that the performance of the UAV positioning system will be improved greatly.INDEX TERMS IMA, unscented Kalman filter, multi-sensor data fusion, UAV positioning system.