When the geometric shadow method is applied to retrieve the significant wave height from marine radar images, the accuracy of shadow segmentation directly affects the performance of wave height estimation. Aiming at this problem, the Rune G′s shadowing algorithm (for the sake of convenience of description, the algorithm proposed by Rune′s method) is improved; an adaptive method that can accurately segment the shadow of the radar images is proposed based on the idea of differential edge detection. This novel method also inherits the advantage of the Rune′s algorithm, and could estimate the significant wave height without any external reference. Compared with the Rune′s method, the partial shadow segmented using the proposed algorithm is more reasonable. The image data acquired from Pingtan Test Base, Fujian were used to verify the effectiveness of the proposed algorithm. The results show that the improved estimation algorithm increases the accuracy of the wave height.