A thorough understanding of the origin and distribution of lithium brine deposits is the foundation for lithium resource exploration, development and utilization. The lithium isotope system, a sensitive geochemical tracer, can be used to track a wide range of geological processes and sources. This study investigates major cations, [Li], and δ7Li of samples (brine lakes, intercrystalline brines, river waters, rain, hot spring waters, spring waters and rocks) from the Qaidam Basin on the northern Tibetan Plateau, China. [Li] values vary from less than 0.01 mg L−1 to ~408.83 mg L−1. There are significant differences in [Li] for different sample types. spring water (rain) < river samples < brine lakes < intercrystalline brines. The δ7Li values of samples display as significant variations as [Li], ranging from 4.33‰ to +40.66‰. There are also significant differences in δ7Li for different sample types. The δ7Li values of spring water and river waters are relatively low and the values are from 4.33‰ to 18.37‰. However, intercrystalline brines and saline lakes have the higher values, and the heaviest δ7Li (+40.66‰) occurs in Chaka Lake. The δ7Li values in brine lakes in the Qaidam Basin show obvious regional distributions, which are also consistent with the structural characteristics of the Qaidam Basin. The possible sources of lithium in the brine lakes of the Qaidam Basin result from multiple mixing of redissolved Li from earlier salt sediments, deep groundwater via fractures (oil field brines, hot springs, etc.), low-temperature weathering processes of Li-rich rock, and freshwater. The results suggest that δ7Li should be a powerful tracer to unravel the sources of Li and reconstruct its accumulation processes in brine lakes. This study provides important theoretical and practical guidance for the effective protection of precious lithium brine deposits and sustainable lithium resource exploration.