Due to underwater complex environment，pile inclination and large measurement error，the determination of underwater cylindrical pile position with high accuracy，low cost and high efficiency has always been a difficulty in offshore engineering. Therefore，this paper proposes a high-precision determination method of underwater cylindrical piles and their spacing distances based on MBES（Multi-beam echo sounder）point clouds. Firstly，we has obtained positions of pile and seabed with low cost and high efficiency using this method. Then，considering the geometric information（normal vector and elevation）as well as pile attribute information，we realized the effective extraction of pile point clouds using a comprehensive threshold segmentation method. A comprehensive determination method of pile center position considering pile shape and measurement error has put forward to realize the high precision determination of pile position and pile spacing. The method in this paper has been verified by practical engineering，and the determination accuracy of pile position and pile spacing is better than 5 cm.