Flood-based hydrodynamic damage to check dam systems on the Loess Plateau of China occurs frequently, and there is a strong desire to carry out risk assessments of such check dam systems. This study proposes a weighting method that combines the analytic hierarchy process, entropy method, and TOPSIS to assess the risk of check dam systems. The combined weight-TOPSIS model avoids weight calculation only considers the influence of subjective or objective preference and the bias of the single weighting method. The proposed method is capable of multi-objective risk ranking. It is applied to the Wangmaogou check dam system located in a small watershed on the Loess Plateau. The result of risk ranking matches the reality of the situation. The gray correlation theory model is utilized to rank the risks in the same research area and compared with the results of the combined weight-TOPSIS model. The combined weight-TOPSIS model is more favorable to risk assessment than the gray correlation theory model. The resolution level and decisive judgment of the combined weight-TOPSIS model are more advantageous. These results are in line with the actual conditions. It proves that the combined weight-TOPSIS model can provide a technical reference for the risk assessment of check dam systems in small watersheds.