Abstract An accurate assessment of sediment transport can assist land and resource managers in any region. The primary objective of this study was to develop a distributed hydrological model for calculating rainfall-runoff coupled with sediment transport to provide a practical method for estimating sediment transport in western Heilongjiang Province, China. The Alun River Basin, which has typical meteorological and hydrological characteristics of western Heilongjiang Province, was chosen as the study area. A sediment transport calculation module was developed based on physically based formulas for the suspended load and bedload, which was coupled with a numerical model of the physical distributed rainfall-runoff process. The model’s ability was validated by comparing the sediment sampling survey results of the particle size group distribution (PSGD) in the flow and the corresponding value of the model calculation results for a control case. The root mean square error (RMSE) and the mean absolute error (MAE) were mostly <10%. The model was used to calculate the rainfall-runoff combined with sediment transport in 2016, and the results indicate that the primary form of sediment transport was as suspended load. The suspended load accounted for over 90% of the total sediment transport caused by the maximum flood peak, and the suspended load accounted for over 80% during the period of normal water level across the selected sections. The sediment transport process was dominated by the runoff process. The contribution of the monthly sediment transport in winter to the annual total value was mostly <1%; while in the rainy season, the contribution of the monthly sediment transport to the annual total value was >15%. The results provide a basis for the assessment of sediment transport and the development of a numerical platform for modeling hydrological processes coupled with land surface processes in western Heilongjiang Province, China.