Abstract: In order to study the applicability of unmanned ship multi-beam bathymetry technology in underwater navigational obstacle detection, taking the underwater obstacle detection of Wuqiao shoal in Pengshui Miao Tujia Autonomous County, Chongqing as an example, QPS Qimera and Terrasolid software were used for data acquisition and processing, and the error of unmanned ship multi-beam point cloud data was compared with the traditional single-beam measurement data. The plane accuracy and elevation accuracy of the unmanned ship multi-beam bathymetry results were analyzed. Combined with the ship′s draft and water level data, the navigational obstacles at different water levels were analyzed. The results showed that the mid-elevation error of the multi-beam bathymetry results of the unmanned ship was -0.027 8 m, the maximum water depth deviation error was ±0.23 m, and 97.3% of the water depth deviation error absolute values were below 0.2 m, which met the requirements of the code. The left bridge hole of Wuqiao in Pengshui does not have the navigation conditions for the time being, and the highest elevation of the top of the steel cylinder that obstacle to navigation is 209.32 m, the lowest is 207.64 m, and it needs to be removed 2.41 m and 0.73m downwards, respectively. According to the elevation of the underwater measurement point in this area, it is necessary to dredge the average depth of 0.10 m in the obstruction area. The unmanned ship multi-beam bathymetry technology can be applied to the detection of underwater obstructions in shallow water areas and can be safer, faster and more reliable compared with the traditional measurement methods.