To understand the magmatic and tectonic events in the Eastern Kunlun Range, we conducted systematic zircon U–Pb geochronology, and paired zircon (ZHe) and apatite (AHe) (U–Th)/He themchronology investigations in the central and eastern segments of this range. Zircon U–Pb ages show two-stage magmatic events of Late Silurian and latest Permian–Early Jurassic. ZHe and AHe ages and multi-system thermochronometers reveal multi-stage rapid cooling events. From a combination of these data with previously published geochronological and thermochronological ages, and regional geological setting, we confirm several important Phanerozoic tectono-magmatic events in this region. Whereas the Silurian granites might be related to a small paleo-ocean subduction and subsequent collision, the latest Permian–Early Triassic granitoids were produced by northward subduction of the Songpan–Ganzi Paleo-Tethyan ocean. The Late Triassic–earliest Jurassic granitoids and Late Triassic–Early Jurassic exhumation are interpreted as response to the collision between Kunlun–Qaidam and Qiangtang. Samples close to the Kunlun Fault show rapid Late Oligocene–Early Miocene exhumation (1.3–1.6 km/Ma), whereas those from the northern part of central segment display extremely low exhumation rates (0.02–0.05 km/Ma). This heterogeneous denudation during 30–20 Ma between northern and southern part of the central segment requires that crustal thickening was completed by lower-crustal underthrusting with little exhumation or crustal thickening in pre-Cenozoic times. The activity of the Kunlun Fault and associated normal faulting component were probably responsible for this stage of rapid exhumation in the southern part. The complex tectono-magmatic evolution of the Eastern Kunlun Range is controlled by pre-Cenozoic paleo-ocean subductions and subsequent continent collisions and Paleogene India–Asia collision. • Zircon U-Pb, apatite and zircon (U-Th)/He ages from the Eastern Kunlun Range. • Zircon U-Pb ages confirm two-stage magmatic events. • Multi-system thermochronometers reveal multi-stage rapid cooling events. • The complex exhumation related to multi-stage tectono-magmatic events.