Background: Shilajit is a commonly used Tibetan medicine, and its water extract is mainly used for various heat-related syndrome, especially that of stomach, liver and kidney. Shilajit is found to exudate from rocks of cliff at an altitude of 2000-4000 m as a water-soluble mixture of black paste and animal feces of Trodocterus spp. or Ochotona spp. Because it is difficult to reach the exudation points so as to explain the its formation process, the source of Shilajit still remains unclear and controversial, which severely impedes its safety and efficacy in clinical application. Methods: In this work, a series of investigations as rock flakes identification, porosity determination, rock mineral analysis, scanning electron microscopy (SEM), and energy dispersive spectrometer (EDS) have been carried out to clarify the source of Shilajit, including the storage condition and exudation process of its organic matter, and to investigate the geological structure of the exudation points as well as physical and chemical characteristics of the mother rocks. Results: The Shilajit exudation points were mainly distributed on the steep cliffs, where there were cavities and sections that could not be eroded by rainwater. The fundamental structure of the exudation points was determined by the rock's bedding planes, joints, fracture surfaces and faults, and developed into micro-topography later. The exudation points were distributed in the Triassic strata and scattered in the Early Mesozoic granitoids. The lithologic features were mainly slate, carbonaceous slate and sandy slate etc. The background rocks were characterized by intergranular pores, dissolved pore, joint and fracture development. Organic matter was widely distributed in these pores and fissures, which had condition for storage and exudation of organic matter. Conclusions: Shilajit mainly distributed on sunny steep slopes and cliffs with a slope of 60° or above at altitude of 2000-4000 m. The lithology character of the Shilajit exudation area were mainly various metamorphic rocks of sedimentary rocks that were rich in organic carbon. The organic matter in Shilajit was found to flow out naturally from rocks along pore, structural plane and even accumulate on the surface of rock as a result of storage environment change caused by rock tectonic action.