Geochemical characteristics of the Chagande’ersi molybdenum deposit in Inner Mongolia and its genesis were analyzed in this study using rock mineralography and rock geochemical testing. The mineralized country rocks of the Chagande’ersi molybdenum deposit consist mainly of medium-to fine-grained monzogranite, medium-to fine-grained rich-K granite, with minor fine-grained K-feldspar granite veins and quartz veins. The rocks are characterized by high silica, rich alkali, high potassium, which are favorable factors for molybdenum mineralization. The rocks have the Rittmann index ranging from 1.329 to 1.961, an average Na2O+K2O value of 7.41, and Al2O3/(CaO+Na2O+K2O)>1, suggesting that the rocks belong to the high-K calc-alkaline peraluminous granite. The typical rock samples are enriched in Rb, Th, K and light rare earth elements, depleted in Sr, Ba, Nb, P and Ti, and these features are similar to that of the melt granite resulting from collision of plate margins. The δEu of the rocks falls the zone between the crust granite and crust-mantle granite, and are close to that of the crust granite; (La/Lu)N indicates the formation environment of granite is a continental margin setting. The Nb/Ta ratios are close to that of the average crust (10); the Zr/Hf ratios of monzogranite are partly below the mean mantle (34–60), while the Zr/Hf ratio of K-feldspar granite are close to the mean value in the crust. Comprehensive analyses show that the granite in this area formed during the transition period between tectonic collision and post-collision. During the plate collision and orogeny, the crust and mantle material were mixed physically, remelting into lava and then crystal fractionation, finally gave rise to the formation of the rock body in this area. This has close spatial and temporal relation with the molybdenum mineralization.