Aiming at the key technical problems of unmanned aerial vehicle(UAV)image calibration and registration, a surface flow field measurement method based on UAV self-calibration is proposed, which is based on structure from motion(SFM)3D reconstruction technology to complete the UAV image self-calibration and speed-up robust features(SURF)method for UAV image registration. The method was applied to measure the surface flow field downstream of the Sancha River Estuary Sluice in Nanjing City. The results show that the accuracy of the 3D reconstruction based on SFM can meet the requirements of self-calibration, and there is no need to set ground control points to calibrate the UAV images, which simplifies the UAV calibration process. SURF method can effectively eliminate the influence of UAV position drift on the surface flow field measurement results.