The Xindigou gold deposit in Inner Mongolia is a medium-sized greenstone type gold deposit but belongs to crisis mine which needs replaceable resources, and hence it is of great significance to evaluate the deep resources. Based on the prospecting and genetic mineralogy theory, the authors analyzed the thermoelectric characteristics of pyrites at different elevations and orebodies using the microscope, electron probe and thermoelectric instrument. Some conclusions have been reached:The pyrite crystals are mainly characterized by cubic, pentadododecahedral and poly-type in the Xindigou deposit, the thermoelectric properties of pyrites, ranging from -331.10 to 340.20 μV·℃^-1, are mainly of the N type, which accounts for about 80%. The ore-forming temperature of the deposit ranges from 250 to 340℃, indicating that the deposit is a medium temperature gold deposit. The thermoelectric parameters of pyrite vary greatly; the degree of denudation varies from 67.96% to 74.31%. According to the spatial distribution of the thermoelectric parameters of the pyrite and the denudation of the orebody, Youlougou orebody may be located at the bottom, and may have a small-scale extension toward the depth. Drill hole ZK106 of Xiaoxigou or body has a better exploration prospect with largescale extension, and drill hole of ZK102 of Xiaoxigou orebody has more potential than ZK2802 of Dahanqing orebody in terms of exploration prospect in the depth. Furthermore, comprehensive results suggest that the deep deposit has good prospecting potential.