The regional surface soil heat flux () estimation is very important for the large-scale land surface process modeling. However, most of the regional estimation methods are based on the empirical relationship between and the net radiation flux. A physical model based on harmonic analysis was improved (referred to as “HM model”) and applied over the Heihe River Basin northwest China with multiple remote sensing data, e.g., FY-2C, AMSR-E, and MODIS, and soil map data. The sensitivity analysis of the model was studied as well. The results show that the improved model describes the variation of well. Land surface temperature (LST) and thermal inertia () are the two key input variables to the HM model. Compared with in situ, there are some differences, mainly due to the differences between remote-sensed LST and the in situ LST. The sensitivity analysis shows that the errors from to in LST amplitude and from to in will cause about 20% errors, which are acceptable for estimation.