Abstract: Understanding the regional groundwater flow field is the fundamental work for the site selection and suitability evaluation of high-level waste geological disposal sites. Due to the wide area and limited data, it is difficult to accurately divide the groundwater flow field in the area, and it also brings trouble to the safety evaluation of the site selection of the high-level waste pre-selection area. To solve this problem, a case study is carried out in the Beishan area of Gansu. The watershed division method, TOUGH2-MP/EOS3 software, which can describe the saturated-unsaturated groundwater flow, and the GRACE satellite data, are used to set up, run and calibrate the model respectively, and the reliability of the model is proved. The results reveal that (1) about 1% of the precipitation infiltrates into the groundwater; (2) topography of the study area is the main factor to determine the groundwater flow, and different precipitation has little impact on the regional groundwater flow field; (3) The regional groundwater flow system can be divided into three sub-systems (Ⅰ, Ⅱ, Ⅲ). The pre-selected area is located in the independent groundwater subsystem III with the minimum area in the south. This study can provide an effective simulation method for the arid area with a huge area and limited measured data, and also an important basis for the safety evaluation of the pre-selected area.