Multiple-objective calibration helps constrain the parameter uncertainties and improve the performances of hydrological models. Previous studies have indicated that calibration toward soil moisture data could improve the streamflow simulation, but its influence on the runoff source apportionment quantification still needs to be analyzed. Meanwhile, although isotope calibration has proved to improve the representation of internal hydrological processes, the value of isotope on the simulation of internal state variables such as soil moisture has yet to be examined. This study utilized the tracer-aided hydrological model THREW-T (Tsinghua Representative Elementary Watershed – Tracer-aided version) in two mountainous basins on the Tibetan Plateau (The Upper Brahmaputra and Upper Yangtze basins) to evaluate the value of soil moisture and isotope data on model calibration. The result shows that: (1) The THREW-T model produced good simulation on streamflow, snow cover area, soil moisture, and stream water isotope simultaneously in the two study areas. Calibration toward soil moisture and isotope caused slight (∼0.03) but statistically significant (p < 0.01) decrease on the Nash-Sutcliffe coefficient of streamflow simulation compared to the baseline calibration variant only toward streamflow. (2) Calibration toward soil moisture brought no improvement to streamflow simulation for the validation period and stations in both basins, only improving soil moisture simulation. However, calibration toward the isotope improved the simulations of internal streamflow and soil moisture's spatiotemporal variation. (3) Different calibration variants resulted in different estimations of the runoff source apportionment, and independent evidence indicated that the results obtained by isotope calibration were most reasonable. Calibrations toward streamflow and soil moisture underestimated and overestimated the contributions from subsurface runoff, respectively. Isotope was the most sensitive objective to the runoff source apportionment and significantly reduced the uncertainty. Our study found a lower value of soil moisture data than the isotope on model calibration. However, we believe that the full potential of soil moisture data was not utilized due to the current limitations in soil moisture simulation and measurement methods, and the development of relevant technologies will make the soil moisture data more valuable for model calibration.