Abstract: To enhance the hydrological monitoring capacity of the tributaries in the Three Gorges Reservoir Area and ensure the completeness of tributaries′ terrain data, this paper proposed to use unmanned vessels to conduct supplementary measurements in the difficult areas of the underwater terrain of the tributaries in the Three Gorges Reservoir Area. The composition, measurement principle, field data collection and indoor data processing procedures of unmanned vessels were introduced. In the practical application of underwater terrain measurement of the tributaries in the Three Gorges Reservoir Area between Fengjie County and Jiangjin in Chongqing, the results of various tests and comparisons were analyzed and presented in depth, and the accuracy was strictly evaluated. The accuracy analysis results show that the measurement accuracy of unmanned vessels can fully meets the requirements of relevant specifications. Unmanned vessels can achieve full coverage measurement of blind spots in the underwater terrain measurement of the tributaries in the Three Gorges Reservoir Area, avoid personnel safety risks, and provide solid data support for the scientific management and dispatching of the Three Gorges Reservoir Area. The research results can provide a reference for the supplementary measurement work of special and complex underwater terrain.