Due to the characteristics of photon-counting LIDAR, there exists range walk error (RWE) when the intensity of the signal fluctuates. In this paper, an effective method to rectify underwater RWE was proposed. The method allows the separation of signal detections from noise detections, and based on a prior model, the method can compensate for RWE. An underwater experiment verified its feasibility and results showed RWE of three parts in a plane was reduced from 75mm to 7mm, from 45mm to 3mm and from 5mm to 0mm, respectively, even when the rate of backscatter photons reached 4.8MHz. The proposed correction method is suitable for high precision underwater photon-counting 3D imaging application, especially when the signal intensity varies sharply.