Gonghe Basin is located in the northeast margin of the Qinghai—Xizang(Tibet) Plateau, in the intersection area of Qinling—Qilian—Kunlun orogenic belt. The heat flow in Gonghe Basin range from 93. 3 mW/m 2 to 111. 0 mW/m 2, with an average heat flow of 102. 2 mW/m 2, which is significantly higher than the other area of China Mainland, about 60. 4 mW/m 2 and its surrounding tectonic units. . There are different understandings about the genetic mechanism of high heat flow in Gonghe Basin, such as crust—mantle magma intrusion, radioactive heat generation, fault tectonic activities and the influence of low- velocity layers in the middle and lower crust. This paper intends to use the existing geological and geophysical data of Gonghe Basin, combined with the newly acquired basin thermophysical parameters, to carry out thermal numerical modeling of Gonghe Basin, and clarify the main factor of influence and control on the high thermal anomaly of Gonghe Basin. Methods: Based on the stratigraphic framework of the Gonghe Basin, the finite element grid model of thermal evolution of the Gonghe Basin is established by combining the deep crustal structure model of the northeastern margin of the Tibetan Plateau and the seismic thermal lithosphere thickness. According to the deep exploration results, the Earth's crust is divided into three layers: upper crust, middle crust and lower crust, each of which is divided into two layers. According to the sedimentary characteristics of the Ghe Basin, the Cenozoic strata are divided into loose Quaternary sedimentary layers in the upper part and Tertiary fluvial lacustrine clastic layers in the lower part. Below the Cenozoic strata is the Indosinian granite intrusive rock layer. The boundary conditions and rock thermal parameters are determined according to the actual detection results. Results: It can be seen from the modeling results that the selection of thermal parameters of the Cenozoic cap layer has a great influence on the thermal structure of Gonghe Basin. By comparing the simulated geothermal temperature curve with the observed geothermal temperature curve, it can be seen that the characteristics of the high geothermal gradient near the surface correspond to the low thermal conductivity of the Cenozoic strata near the surface, indicating that the low thermal conductivity of the quaternary strata is an important factor controlling the high geothermal gradient. At the same time, Gonghe Basin is located at the junction of Qinling—Qilian—Kunlun orogenic belt, and the influence of deep processes below the lithosphere provides a certain degree of regional thermal anomaly background for the high thermal anomaly in Gonghe Basin. Conclusions: The mechanism of the high thermal anomaly in this basin is explored by the numerical thermal modeling of Gonghe Basin. If the Cenozoic strata are considered as a whole, the numerical analysis results show that the measured thermal conductivity parameters are not enough to form the high heat in the Gonghe Basin, and there must be the influence of deep heat sources, such as middle and lower crust melt. If the Cenozoic strata are divided Quaternary and Tertiary, the modeling results shows the main controlling factor of the formation of high thermal anomalies in the basin is the very low thermal conductivity of the loose Cenozoic sediments, which is consistent with the actual measured with the geothermal curve.