Stable boundary layer height (SBLH) is an important parameter to characterize the characteristics and vertical structure of the nocturnal lower atmosphere at night. The distribution of SBLH has obvious spatial and temporal differences, and there are many meteorological factors affecting the SBLH, but at present, there are few quantitative studies on the effects of near-surface meteorological factors on the SBLH in the desert hinterland. This study was based on GPS sounding balloon data, near-surface meteorological observation data, and ERA5 data from Tazhong Station (TZ) in the Taklamakan Desert (TD) collected in July 2017, 2019, and 2021. The variation characteristics of the SBLH and its relationship with near-surface meteorological factors are described. We quantitatively analyzed the degree of influence of near-surface meteorological factors affecting the SBLH and verified it using a model. The study also elucidates the possible formation mechanism of the SBLH in the TD hinterland. The SBLH in the TD hinterland trended upward in July 2017, 2019, and 2021, which is consistent with the changes in meteorological factors, according to the near-surface meteorological observation and ERA5 data. Therefore, we think that an inherent connection exists between near-surface meteorological factors and the SBLH. The results of correlation analysis show that complex internal connections and interactions exist among the meteorological factors near the ground; some thermal, dynamic, and other meteorological factors strongly correlate with the SBLH. Having established the change in SBLH (ΔSBLH) and in major thermal, dynamic, and other meteorological factors (Δ), the linear regression equation between them revealed that near-surface meteorological factors can affect the SBLH. The dynamic factors have a stronger influence on the ΔSBLH than thermal and other factors. The results of model validation based on the variable importance projection (VIP) also confirmed that the SBLH in the TD hinterland is jointly affected by dynamic and thermal factors, but the dynamic factors have a stronger impact. The mechanism through which the SBLH forms is relatively complex. At night, surface radiative cooling promotes the formation of a surface inversion layer, and low-level jets strengthen wind shear, reducing atmospheric stability. The combined effects of heat and dynamics play an important role in dynamically shaping the SBLH. This study helps us with accurately predicting and understanding the characteristics of the changes in and the factors influencing the SBLH in the TD hinterland, providing a reference for understanding the mechanism through which the SBLH forms in this area. At the same time, it provides a scientific basis for regional weather and climate simulation, meteorological disaster defense, air quality forecasting, and model parameterization improvement.