Hot dry rock (HDR) is an important geothermal resource and clean energy source that may play an increasingly important role in future energy management. High-temperature HDR resources were recently detected in deep regions of the Gonghe Basin on the northeastern edge of the Tibetan Plateau, which led to a significant breakthrough in HDR resource exploration in China. This research analyzes the deep temperature distribution, radiogenic heat production, heat flow, and crustal thermal structure in the Qiaboqia Valley, Guide Plain, and Zhacanggou area of the Gonghe Basin based on geothermal exploration borehole logging data, rock thermophysical properties, and regional geophysical exploration data. The results are applied to discuss the heat accumulation mechanism of the HDR resources in the Gonghe Basin. The findings suggest that a low-velocity layer in the thickened crust of the Tibetan Plateau provides the most important source of constant intracrustal heat for the formation of HDR resources in the Gonghe Basin, whereas crustal thickening redistributes the concentrated layer of radioactive elements, which compensates for the relatively low heat production of the basal granite and serves as an important supplement to the heat of the HDR resources. The negative effect is that the downward curvature of the lithospheric upper mantle caused by crustal thickening leads to a small mantle heat flow component. As a result, the heat flows in the Qiaboqia Valley and Guide Plain of the Gonghe Basin are 106.2 and 77.6 mW/m2, respectively, in which the crust-mantle heat flow ratio of the former is 3.12:1, indicating a notably anomalous intracrustal thermal structure. In contrast, the crust-mantle heat flow ratio in the Guide Plain is 1.84:1, which reflects a typical hot crust-cold mantle thermal structure. The Guide Plain and Zhacanggou area show the same increasing temperature trend with depth, which reflects that their geothermal backgrounds and deep high-temperature environments are similar. These results provide important insight on the heat source mechanism of HDR resource formation in the Tibetan Plateau and useful guidance for future HDR resource exploration projects and target sites selection in similar areas.