To investigate the late Cenozoic convergence between the Pamir and Tianshan orogenic systems, 14 rock samples were collected in 2022 from the North Pamir–South Tianshan convergence zone in northwestern China. This dataset (Table S3) contains apatite fission-track (AFT) thermochronology data for 14 samples acquired between 2023 and 2025 in Germany and the United States using the external detector method (EDM). Sample preparation, mount polishing, and apatite etching were conducted at the University of Potsdam, Germany. Apatite mounts were etched for 20 s in 5.5 N HNO₃ at 21°C, packed with external mica detectors and CN5 uranium dosimeter glasses, and subsequently irradiated with thermal neutrons at Oregon State University, USA. Following irradiation, the mica detectors were etched for 45 min in 40% HF at 21°C at the University of Potsdam. Spontaneous and induced fission tracks were counted, and confined-track etch pit diameters (Dpar) were measured using a Zeiss optical microscope at 1250× magnification coupled with FTStage software. The dataset includes AFT ages, Dpar measurements, age calculations, and associated analytical uncertainties (1σ). These data provide constraints on late Cenozoic exhumation and deformation history of the North Pamir–South Tianshan convergence region.