The Changning–Menglian suture represents a remnant of the main Paleo-Tethys in the Sanjiang Orogen (SW China), and preserves abundant magmatic rocks formed during orogenic processes related to the closure of the Paleo-Tethys. Our geochronology study on granitoids of the Lincang Batholith, a prominent magmatic feature along the Changning-Menglian suture, yields crystallization age of 261 ± 1 Ma, 252 ± 1 Ma, to 203 ± 1 Ma, confirming a multi-stage emplacement of the batholith. The Late Permian granodiorites are medium- to high-K calc-alkaline, metaluminous (A/CNK = 0.99–1.10), with high Al2O3 content (14.03 wt%), high Mg# (46), high (87Sr/86Sr)i (0.7192–0.7278), negative whole-rock εNd(t) (− 14.7 to − 8.5), (206Pb/204Pb)t of 18.199 to 18.791, (207Pb/204Pb)t of 15.714 to 15.765, (208Pb/204Pb)t of 38.500 to 38.851, zircon δ18OSMOW = 7.13‰–8.57‰ and zircon εHf(t) of − 14.8 to + 0.4. The Late Triassic granites are characterized by high SiO2 value (68.52 wt%), high Mg# values of 50, with negative Eu anomalies (δEu = 0.32–0.78), high (87Sr/86Sr)i (0.7202–0.7424), negative whole-rock εNd(t) (− 15.6 to − 10.7), (206Pb/204Pb)t of 18.659 to 18.793, (207Pb/204Pb)t of 15.752 to 15.791, (208Pb/204Pb)t of 38.865 to 38.959, zircon δ18OSMOW = 8.07‰–9.76‰. These geochemical and isotopic features suggest that the primary magma of both Late Permian and Late Triassic granitoids most likely originated from partial melting of the underlying Proterozoic crustal rocks, with limited addition of mantle components. Our new geochronological and geochemical results together with previously published data, suggest that the composite Lincang Batholith records three magmatic episodes related to the Paleo-Tethys evolution, corresponding to subduction (prior to ~ 252 Ma), syn-collisional (250–237 Ma), and post-collisional (235–203 Ma) stages.