The Yangla deposit is an intrusion‐related Cu deposit in the Jinshajiang tectonic belt (eastern Sanjiang region, SW China). Despite extensive studies that have been conducted on this deposit, the relationship between the granitic magma and Cu mineralization is still unclear, and hence, the genesis is debated. To answer this question, we conducted an integrated study of mineralogy, fluid inclusions (FIs), and hydrogen and oxygen (H‐O) isotopes. Three mineralization stages were identified based on the ore textures, alteration zonation, and crosscutting relationships: (i) pre‐ore prograde skarn (stage I), with the garnet and pyroxene dominated by andradite and diopside, respectively; (ii) syn‐ore retrograde alteration (stage II), which is subdivided into the early syn‐ore stage (stage IIa) marked by retrograde hydrated mineral assemblages and significant Fe‐Cu‐Mo‐Pb‐Zn sulfide mineralization, and the late syn‐ore stage (stage IIb) featured by quartz‐calcite veins; and (iii) late supergene mineralization (stage III), which is characterized by secondary azurite and malachite. These results of mineralogy, FIs, and H‐O isotopes indicate that: (i) Cu mineralization has a close temporal, spatial, and genetic relationship with skarn alteration; (ii) the ore fluids were magmatic dominated with late‐stage meteoric water incursion; and (iii) Type‐S (halite‐bearing) and Type‐V (vapor‐rich) FIs coexisted in garnet and clinopyroxene of stage I, indicating that fluid boiling might have occurred during this stage. From stage I to stage IIa, the FI type transformed from Type‐S + Type‐V + Type‐L (liquid‐rich) to Type‐V + Type‐L with the conduct of mineralization and was accompanied by the disappearance of Type‐S, and homogenization temperature and salinity also tended to decrease dramatically, which may be caused by the deposition of skarn minerals. At stage IIa, boiling of the ore fluids still continued due to the change from lithostatic to hydrostatic pressure, which triggered the precipitation of abundant quartz‐Cu‐Mo‐Fe sulfides. Furthermore, fluid mixing between a high‐temperature magmatic fluid and a low‐temperature meteoric water might cause a considerable drop in temperature and the deposition of Cu‐bearing quartz/calcite veins during stage IIb. Hence, we consider the Yangla deposit to be of a skarn type, genetically related to the Mesozoic magmatism in the Sanjiang region.