The spatial heterogeneity of soil salinity is of great significance to understand the spatial distribution of salinity in inland salt marsh wetlands and its response mechanism to the environment. In this paper, the classical statistics, geostatistical, and Kriging interpolation were used to study the interaction between the spatial heterogeneity of the total salt content in the 0-50 cm soil layer of the shallow section the Sugan Lake salt marsh and the depth of the groundwater level and the vegetation coverage. The research area was located in Sugan Lake wetland at the intersection of the Altun Mountains and the Qilian Mountains in the northwest of the Qaidam Basin (94°10'33″-94°14'43″E, 39°01'25″-39°05'32″N), and the elevation is between 2795-2808 m. The results indicates that: (1) the average values of total salt content in the soil layers of 0-10 cm, 10-30 cm and 30-50 cm in the Sugan Lake wetland are (204.41±11.8) g/kg, (18.62±0.92) g/kg, and (15.89±0.81) g/kg, respectively. (2) With the increase of soil depth, the variation of soil total salt content changes from strong to weak. Random spatial variability and total heterogeneity degree change from high to low, which has strong spatial correlation under the influence of structural factors. The range of variation is between 5.2-8.49 km. The total salt content of 0-10 cm, 10-30 cm has anisotropic characteristics, while the anisotropy ratio of 30-50 cm is close to 1, showing isotropy. (3) There is a strong spatial heterogeneity of soil total salt content in each layer, and the high and low value centers distributed in the patches. The total salt content of soil is positively correlated with groundwater depth, and highly significantly negative correlated with the vegetation coverage (P<0.01). The spatial heterogeneity of soil total salt content in inland salt marsh wetland of Sugan Lake is mainly influenced by vegetation coverage. The variation of groundwater depth increases the complexity of its spatial variability, which reflects the complexity and heterogeneity of the soil physical and chemical spatial system of inland salt marsh wetland.