A low-density rain gauge network is always a major obstacle for hydrological modelling, particularly for alpine and remote regions. The availability of the Tropical Rainfall Measuring Mission (TRMM) rainfall products provides an opportunity for hydrological modelling, although the results must be validated and corrected before they can be used in further applications. In this paper, the combination of proportional coefficients with cross-checking by hydrological modelling was proposed as a method to improve the quality of TRMM data in a rural mountainous region, the Hotan River Basin. The performance of the Soil and Water Assessment Tool (SWAT) model was examined using streamflow and snow cover measurements. The corrected results suggest that the proportional coefficient approach could effectively improve the TRMM data quality. A verification of the hydrological model outputs indicated that the simulated streamflow was consistent with the observed runoff. Moreover, the modelled snow cover patterns presented similar spatial and temporal variations to the remotely sensed snow cover, and the correlation coefficient ranged from 0.63 to 0.98. The results from the TRMM correction and hydrological simulation approach indicated that this method can significantly improve the precision of TRMM data and can meet the requirements of hydrological modelling.