Aiming at the low accuracy of lake contour extraction from two-dimensional images of the existing algorithms for analyzing the geometric information of lakes, a lake extraction algorithm based on three-dimensional convolutional neural network was proposed. Firstly, based on the flatness information, the candidate lakes were located from the laser scanning point clouds, and the candidate points were organized as voxels to be an input of the neural network. Meanwhile, the non-lake areas were filtered from candidate areas by the deep learning technique. Then, based on the chain-code algorithm, contours of lakes were extracted from point clouds and their geometry information was analyzed. The experimental results show that, the accuracy of the proposed algorithm in extracting lakes from laser scanning point clouds is 96.34%, and compared with the existing extraction algorithm for two-dimensional images, the proposed algorithm can calculate and analyze the shape information of lakes, which provides convenience for lake monitoring and management.