As the junction of the Silk Roads, the Tarim Basin played a critical role in human migration and cultural interaction between the East and the West. Recently, population migration patterns have been increasingly reconstructed from strontium isotope ratios (87Sr/86Sr) in archaeological human skeletons, and further constraints on their provenance require a bioavailable 87Sr/86Sr map across the basin. Based on measurement data from 44 river samples in this study and 29 samples from published data, we generate the first map of bioavailable 87Sr/86Sr values across the Tarim Basin and the neighbouring area. From the baseline map, three geologically distinct regions can be identified: (1) the Yili Block, Tian Shan orogenic belt and northern Tarim Block with lower ratios (0.7105 ± 0.0007 (1σ), n = 25); (2) the southern Tarim Block with higher ratios (0.7118 ± 0.0008, n = 29); and (3) the eastern Pamir Block with diverse values (0.7110 ± 0.0009, n = 19). This map is a promising tool for recognizing the origins of immigrants in the Tarim Basin and may aid understanding of the migration patterns and cultural communication along the Silk Roads.