The decoherence effect of a laser caused by a speckle field seriously restricts the development of heterodyne lidar. To address this problem, we proposed a spatial decoherence compensation algorithm, whose feasibility was proved by experiments with a system featuring simple structure and convenient operation. The results demonstrated that the speed of the proposed algorithm was several orders higher than that of other algorithms and the system SNR was increased by a maximum of 1464 times after the algorithm processing. The proposed algorithm can process the signal in real time and effectively, having great application potential in long-distance weak target detection.