Glacier changes are driven by glacier melt, which in turn affects streamflow. This paper describes an accounting scheme for glacier area change distribution across elevation profiles for application in the glacier module of the Soil and Water Assessment Tool (SWAT) model. In addition to volume-area scaling relationship in the module, the paper introduced volume-length scaling relations to estimate changing glacier terminus and update glacier area changes between equilibrium line altitude (ELA) and the terminus. The improved scheme was used in the nested Urumqi Glacier No. 1 catchment and Urumqi River Basin in Tienshan Mountains, China. Comparison of the simulated and observed data suggested that the new scheme accurately reproduced the length and area changes of Glacier No. 1. The contributions of glacier melt and ice melt to runoff were estimated at 71% and 38% for Glacier No. 1 Hydrological Station and 11.1% and 5.8% for Yingxiongqiao Hydrological Station, respectively. This helped to better interpret long-term monitored glacio-hydrological processes of Glacier No. 1 and the variation of glacier melt contribution to streamflow at the catchment scale.