This paper reports new geochronological (U–Pb) and isotope (C, O, and S) data to investigate the timing of mineralization and mode of ore genesis for the recently discovered Changtuxili Mn–Ag–Pb–Zn deposit, located on the western slopes of the southern Great Hinggan Range in NE China. The mineralization is hosted by intermediate–acidic lavas and pyroclastic rocks of the Baiyingaolao Formation. Three stages of mineralization are identified: quartz–pyrite (Stage I), galena–sphalerite–tetrahedrite–rhodochrosite (Stage II), and quartz–pyrite (Stage III). δ13C and δ18O values for carbonate from the ore vary from −8.51‰ to −4.96‰ and 3.97‰ to 15.90‰, respectively, which are indicative of a low-temperature alteration environment. δ34SV-CDT values of sulfides range from −1.77‰ to 4.16‰ and show a trend of equilibrium fractionation (δ34SPy ​> ​δ34SSp ​> ​δ34SGn). These features indicate that pyrite, sphalerite, and galena precipitated during the period of mineralization. The alteration mineral assemblage and isotope data indicate that the weakly acidic to weakly alkaline ore-forming fluid was derived largely from meteoric water and the ore-forming elements C and S originated from magma. During the mineralization, a geochemical barrier was formed by changes in the pH of the ore-forming fluid, leading to the precipitation of rhodochrosite. On the basis of the mineralization characteristics, new isotope data, and comparison with adjacent deposits, we propose that the Changtuxili Mn–Ag–Pb–Zn deposit is an intermediate-to low-sulfidation epithermal deposit whose formation was controlled by fractures and variability in the pH of the ore-forming fluid. The surrounding volcanic rocks yield zircon U–Pb ages of 160−146 ​Ma (Late Jurassic), indicating that the mineralization is younger than 146 ​Ma.