Alpine glaciers are sensitive indicators of regional climate change, which can affect regional ecological stability and social development. Variations in glacier mass balance (GMB) are an important parameter in studying glacier change. In this study, data from the Ice, Cloud, and Land Elevation Satellite-1 (ICESat-1), the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2), and CryoSat-2 (Ku-band) were combined, and high-resolution ALOS DEM was employed to denoise. After that, the polynomial fitting method was used to analyze the characteristics of glacier surface elevation (GSE) variations from 2003–2020 in the Tomur Peak Region of the Central Asian Tianshan Mountains and the regional GMB was calculated. Research results showed that: (1) From 2003–2020, the GSE of the Tomur Peak Region had an overall −8.95 ± 4.48 m variation, the average rate of which was −0.53 ± 0.26 m/yr (/yr is /year). Overall, elevations of most glaciers in the Tomur Peak Region had downward trends, with a rate of change of −0.5 to 0 m/yr. The fastest rate of elevation decline in the Koxkar Glacier Tongue was −1.5 m/yr. The elevation of some altimetric points in the Eastern Tomur Peak Region showed a rising state, with a maximum rate of variation of 1.0 m/yr. (2) From 2003–2020, the average GMB in the Tomur Peak Region was −1.51 ± 0.04 Gt/yr. In the region of elevation below 4000 m, small glaciers dominated, with a GMB of −0.61 ± 0.04 Gt/yr. With increasing elevation, the melting rate of glaciers gradually slowed down, but overall, the mass balance remained in a state of decline. (3) Climate was the main driving factor of GMB change in the study area. From 2003–2020, in the Tomur Peak Region, the average annual temperature continued to increase at a rate of 0.04 ± 0.02 °C/yr, and this was the main influencing factor for the negative GMB in the Tomur Peak Region. In the same period, the annual precipitation showed a rising trend with a linear variation rate of 0.12 ± 0.06 mm/yr, and the rising precipitation was the influencing factor for the gradually slowing change in the GMB in the study area.