The water conservation of the water source region in the upper reaches is the key to the sustainability of the landscape of Hani Terraces. The heterogeneity of soil moisture is an important indicator to reveal the pattern of water conservation. Using the grid sampling method, we collected 162 samples (81 in the dry season, 81 in the rainy season) from surface soil (0-20 cm) of the water source region, and analyzed the spatial variability of soil moisture on Hani Terraces based on classical statistics and geostatistics method. The results indicated that: (1) Soil moisture in the dry season is of moderate variation (Cv is 18.19%), the ratio of semivariogram’s structure is 99.9%, and the range is 383 m. Soil moisture in the rainy season is also of moderate variation (Cv is 18.50%), the ratio of semivariogram’s structure is 99.9%, and the range is 475 m, indicating a high spatial autocorrelation of soil moisture. From the dry season to the rainy season, the spatial structure parameters of soil moisture are different, and the most obvious one is the range. There is a consistency of the anisotropy, but the ratio is different. (2) Kriging interpolation figure indicates that soil moisture’s spatial pattern in the dry season shows obvious patches with high fragmentation and poor continuity of space. Soil moisture’s spatial pattern in the rainy season shows stripes with good continuity of space. The overall trends of the soil moisture pattern are consistent in the two seasons, but the spatial pattern of the dry season is more significant and is almost same as the land use pattern. (3) Soil moisture and its variation are consistent regarding their spatial tendencies in the dry and rainy seasons because they are both affected by rainfall, but the response of soil moisture in the dry season is more sensitive to rainfall. (4) Land use types are the key factors affecting the heterogeneity of soil moisture, but meteorological factors (such as rainfall) can reinforce or weaken that trend. Soil moisture is significantly correlated with the elevation, but less affected by the slope gradient. (5) Spatial and temporal variability of soil moisture can reflect the differences of water conservation pattern, being of great significance in identifying the key water conservation region, protecting the ecological security pattern, and maintaining the balance of water supply and the stability of the terrace landscape.