Western Yunnan is composed of several extruded continental microblocks that were generated by the oblique collision between the Indian and Asian continents during the Cenozoic. In this study, the magmatic and tectonic frameworks of western Yunnan in the Cenozoic were analyzed based on geochemistry, Sr–Nd–Pb isotopes, and apatite/zircon fission track dating. Magmatism during the Cenozoic in western Yunnan was then divided into three distinctive episodes: alkali granite rocks produced from 55 to 46 Ma were derived from the anatexis of crustal materials; bimodal igneous rocks formed between 37 and 24 Ma were possibly derived from an EMII mantle with a contribution from continental materials; and intermediate–basic volcanic rocks produced in the Tengchong microblocks since ~16 Ma are considered to be generated by the partial melting of the upper mantle that was induced by the pulling apart of the dextral Gaoligong strike–slip fault system. Moreover, fission track analysis of apatite and zircon indicates that the regional crustal uplift in western Yunnan possibly began at ~34 Ma, with accelerated annealing occurring at ~24 Ma, ~13 Ma, and ~4 Ma. During the past 24 Ma, the average denudation rate was ~0.32 mm/yr for the faulted block controlled by the Chongshan–Lancang River fault. However, crustal uplift has been relatively gentle in places lacking influence from strike–slip shear zones, with an average denudation rate of ~0.2 mm/yr. Combined with strike–slip shear and block rotation in the Cenozoic, the tectonic evolution of western Yunnan since ~45 Ma can thus be divided into four stages occurring at 45–37 Ma, 37–24 Ma, 24–13 Ma, and 13–0 Ma.