Maodeng deposit is a large-sized Mo-Bi-Sn-Cu deposit located in the Xinlinhot of Inner Mongolia in the southern segment of the Great Xing’an Range. The ore-forming elements in the deposit are found in the volcanic breccia of Lower–Middle Permian Dashizhai Formation and granite porphyry of the Alubaogeshan complex, constituting distinct regional mineralization zones such as hydrothermal vein-type of Sn-Cu orebodies in the upper parts and stockworks, veinlets and disseminated-type of Mo-Bi orebodies in the lower parts. This paper has conducted an integrated study using a comprehensive field survey, molybdenite Re-Os age, fluid inclusion, and isotopic (O, H, S, and Pb) analyses. The mineralization in the deposit can be divided into four stages, which are molybdenite-native bismuth-quartz (stage I), cassiterite-wolframite-topaz-quartz (stage II), chalcopyrite-sphalerite-galena-fluorite-sericite-quartz (stage III) and stibnite-pyrite-quartz-fluorite (stage IV). The Re-Os isochron age of four molybdenite samples was estimated as 139.2 ± 3.9 Ma, indicating the deposit was formed during the Early Cretaceous. The Maodeng deposit is characterized by three kinds of fluid inclusions (FIs): liquid-rich two-phase, vapor-rich two-phase, and daughter mineral-bearing three-phase FIs. The homogenization temperatures for the FIs of stages I through IV are 292–387 °C, 222–333 °C, 172–252 °C, and 122–197 °C, with calculated salinities of 4.2–43.6 wt%, 2.1–38.9 wt%, 1.9–33.6 wt% and 0.7–5.1 wt% NaCl equiv., respectively, showing the gradual reduction in temperature and salinity of hydrothermal fluids. Hydrogen and oxygen isotopic data of quartz indicate that the dominant origin of the ore-forming solutions from deep granitic intrusions followed by their dilution by limited meteoric water. The sulfides have δ34S values ranging from − 6 ‰ to − 0.49 ‰, and have 206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb ratios similar to those of K-feldspars from the Alubaogeshan pluton, suggesting the primary origin of ore-forming materials of the Maodeng deposit are magmatic. Molybdenite and native bismuth may precipitate primarily by fluid boiling, chalcopyrite could deposit mainly by fluid mixing, and cassiterite precipitate mainly through fluid boiling and mixing.