To investigate the late Cenozoic convergence between the Pamir and Tianshan orogenic systems, 15 rock samples were collected in 2022 from the North Pamir–South Tianshan convergence zone in northwestern China. This dataset (Table S2) contains 49 single-grain zircon (U–Th)/He (ZHe) analyses acquired between 2023 and 2025 in Germany. Individual zircon grains were encapsulated in niobium (Nb) tubes and degassed using an ASI Alphachron helium extraction and analysis system at the University of Potsdam. Following helium measurement, the degassed capsules were subjected to standard four-acid digestion in high-pressure autoclaves. Uranium (U), thorium (Th), and samarium (Sm) concentrations were determined by isotope dilution and measured using a Thermo Element 2XR high-resolution inductively coupled plasma mass spectrometer (HR-ICP-MS) at the Element and Isotope Geochemistry Laboratory (ElMiE), GFZ Helmholtz Centre for Geosciences, Potsdam. The analytical results were used to calculate single-grain ZHe ages, as well as sample-average and weighted-mean ages reported in this dataset. These data provide constraints on the exhumation and deformation history of the North Pamir–South Tianshan convergence region during the late Cenozoic.