Head-cut erosion is the primary mechanism causing overtopping-induced breaches of check dams. Furthermore, the dam fill soil properties directly influence the head-cut migration rate. Although the fill materials of most flume model tests are cohesive soils, there are no experimental studies on loess materials with low erosion resistance. Accordingly, this study conducted 26 groups of flume model tests on the check dam head-cut migration mechanisms. Furthermore, it comprehensively analyzed the factors influencing the characteristics of head-cut migration in check dams, namely compactness, water content, inflow, and head-cut height, from the macro-and micro-viewpoints. The head-cut erosion rate models of compacted loess were developed considering multiple factors. A nonlinear multiple head-cut migration coefficient regression model was developed using the energy dissipation theory, the findings from the head-cut erosion tests, and experimental results from other studies, while considering the water content, compactness, clay content, inflow, and head-cut height as inputs. Seven sets of measured data with different erosion resistances were selected to verify the rationality and accuracy of the proposed model. In general, the sensitivity analysis results showed that the model could be used for cohesive soil with strong erosion resistance and silty sand and loess with weak erosion resistance. Its generalization and prediction accuracy have been further improved compared to other models of the same type.