As a heavily glaciated region, the Eastern Pamir plays a crucial role in regional water supply. However, considerable ambiguity surrounds the distribution of glacier ice thickness and the details of ice volume. Accurate data at the local scale are largely insufficient. In this study, ground-penetrating radar (GPR) was applied to assess the ice thickness at Muztagh Glacier No.16 (MG16) in Muztagh Ata, Eastern Pamir, for the first time, detailing findings from four distinct profiles, bridging the gap in regional measurements. We utilized a total of five different methods based on basic shear stress, surface velocity, and mass conservation, aimed at accurately delineating the ice volume and distribution for MG16. Verification was conducted using measured data, and an aggregated model outcome provided a unified view of ice distribution. The different models showed good agreement with the measurements, but there were differences in the unmeasured areas. The composite findings indicated the maximum ice thickness of MG16 stands at 115.87 ± 4.55 m, with an ice volume calculated at 0.27 ± 0.04 km3. This result is relatively low compared to the findings of other studies, which lies in the fact that the GPR measurements somewhat constrain the model. However, the model parameters remain the primary source of uncertainty. The results from this study can be used to enhance water resource assessments for future glacier change models.