The use of VR technology to realize the innovative presentation of canal landscapes is an effective technical means to inherit the cultural heritage of canals. In order to improve the accuracy and efficiency of point cloud alignment in virtual modeling, this paper takes advantage of feature alignment, and the ICP algorithm to find the optimized starting position using the SAC-IA algorithm and then adopts the ICP algorithm to carry out fine alignment and on the basis of which, a virtual reality system Analysis shows that the alignment method adopted in this paper demonstrates better accuracy and efficiency than similar algorithms in both coarse and fine alignment tests. Applying the constructed virtual canal culture presentation system for knowledge education, it is found that the students in the experimental group have a better grasp of knowledge related to canal culture and learn more efficiently, and the quantitative scores of satisfaction in the four dimensions of learning method, learning efficiency, learning interest, and learning content are 4.85, 4.7, 4.7, and 4.6, which indicate that the system helps to increase people’s interest in the cultural heritage of canals.