The water movement of frozen soil shows its uniqueness due to the influence of freeze-thaw process. However, there is a lack of in-depth study on soil moisture infiltration characteristics of different types of frozen soil at present. Therefore, a slope cross-section at the small basin of Kangqiong in Source Area of the Yellow River is studied. This zone on the upper slope is covered by seasonally frozen ground and that on the down slope is covered by the permafrost. Based on the field observation, the data has been collected from various sources including atmospheric precipitation, soil moisture, and suprapermafrost water from May 2017 to October 2017. In addition, the soil moisture infiltration is numerically simulated by the freeze-thaw module of HYDRUS-1D software package. Based on seasonal rainfall variation, the difference of soil moisture infiltration in permafrost regions and seasonally frozen regions is statistically investigated during thawing period. The results are summarized in the following: 1) in the rapid thawing stage, the rainfall infiltration is dominated by surface runoff. The water content of surface soil increases, but the infiltration of soil is limited. So, the suprapermafrost water flow rises slightly. During the stable thawing stage, soil water content increases and soil moisture infiltration increases. Influenced by the barrier of permafrost layer, the suprapermafrost water flow in permafrost regions rises greatly. While in seasonally frozen regions, the soil moisture infiltration is dominated by deep leakage or lateral flow. 2) Influenced by rainfall intensity, soil texture, evapotranspiration and vegetation coverage, the rainfall loss is mainly caused by surface runoff. Soil moisture content of each layer on the down slope increases gradually from top to bottom with the thawing of frozen soil and reaches the saturation state. Soil moisture content in surface layer on the upper slope has been rising with time, but it can not reach a stable state. 3) The existence of regional talik groundwater leads to a small increase of the suprapermafrost water level on the upper slope. In addition to rainfall infiltration, the change of the suprapermafrost water on the down slope is also affected by talik groundwater, which causes the rapid rise of the suprapermafrost water level on the down slope. The results are helpful to understand the degradation of frozen soil and its hydrological effects under the background of global climate change. At the same time, it will provide scientific basis for quantitative assessment of water resources vulnerability and regional ecological sensitivity.