Soil water is the key factor of eco-environmental restoration in the water-wind erosion crisscross region of the Loess Plateau, which demonstrates a great temporal and spatial heterogeneity. In this study, the representative LaoYeManQu watershed in the water-wind erosion crisscross region was selected as the research area, and 73 sampling points were set up with a grid of 50 m×50 m. From June 2013 to October 2019, 23 in-situ observations of soil water content (SWC) in 0-5 m profile was carried out by using neutron probe, and the environmental factors of each sampling point were collected simultaneously. Combined with classical statistics, geostatistics, and random forest, the seasonal variation characteristics and controlling factors of SWC at different soil layers (5 layers in total, one layer per meter) in the watershed were investigated. The results showed that the distribution characteristics and seasonal variations of SWC for soil layers differed. For the 0-1 m soil layer, the mean SWC between summer and winter was significant different (p < 0.05); while below 1 m, the mean SWC in spring was higher than that in other seasons, but it was not significant. In the soil layers above 3 m, significant differences were found in SWC among different land uses and between loam and sandy soil for four seasons (p < 0.05). For each soil layer, the SWC between shady and sunny slopes also differed significantly in different seasons (p < 0.05). SWC in all seasons was negatively correlated with soil bulk density and sand content, and positively correlated with other measured factors. With the increasing of soil depth, the correlations between SWC and measured factors generally decreased except soil organic carbon density and clay content. The factors contributing to SWC variation were soil properties, topography, and land use in sequence. These results could provide reference for the management of deep soil water resources, soil hydrological observation and simulation, and vegetation optimization in the study area and other similar regions characterized by the water and wind erosion crisscross.