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In this study, Shengli fault depression, Tangyuan fault basin, and northern Songliao Basin in Yitong?Yilan fault zone of Heilongjiang province are considered the research areas for geothermal anomaly. Based on the temperature of the deep thermal reservoir, the hydrothermal fluid channel, caprock thickness, and the mode of heat transfer, which are the main factors controlling the geothermal reservoir formation, we examined geothermal resource system of the underground HDR in this area. First, we inversed the aeromagnetic data, calculated the Curie isotherm depth, analyzed the geothermal distribution characteristics, and estimated the temperature of the deep heat source. Second, we applied the controlled source audio frequency magnetotelluric (CSAMT) and magnetotelluric (MT) methods to obtain the deep electrical structure of the study area. We determined the thickness of the caprock and the hydrothermal fluid channel. Finally, we obtained the borehole geothermal steady-state temperature measurement data and water sample chemical analysis data from the logging temperature curves of 24 wells to infer the mode of heat transfer. Based on the results, we built a model of the geothermal system of the sedimentary basin in this area. The results show that the depth of Curie isotherm in the study area is 17–39 km. The resistivity of sedimentary caprock in the north of Songliao basin is low, and there exists a deep heat source, which is mainly thermal convection. In contrast, in Shengli and Tangyuan fault basins, heat conduction is dominant. Based on the geothermal system model, we conclude that the area from Daqing to Lindian in Songliao basin has a thermal-convection-dominated sedimentary basin geothermal system. Heat exchange is realized by the upwelling of mantle-derived thermal materials through fracture channels. The thick sedimentary caprock reduces the heat loss. It can be a target for sustainable development and utilization of HDR.