The source region of the Yellow River (SRYR) located in the northeast of the Qinghai-Tibetan Plateau is not only the largest runoff-producing area in the Yellow River Basin, but also the most important freshwater-supply ecological function area in China. In this study, the short-term spatiotemporal distribution of selected legacy and alternative perfluoroalkyl acids (PFAAs) in the SRYR was first investigated in multiple environmental media. Total PFAA concentrations were in the range of 1.16-14.3 ng/L, 4.25-42.1 pg/L, and 0.21-13.0 pg/g dw in rainwater, surface water, and sediment, respectively. C4-C7 PFAAs were predominant in various environmental matrices. Spatiotemporal characteristics were observed in the concentrations and composition profiles. Particularly, the spatial distribution of rainwater and the temporal distribution of surface water exhibited highly significant differences (p<0.01). Indian monsoon, westerly air masses, and local mountain-valley breeze were the driving factors that contributed to the change of rainwater. Rainwater, meltwater runoff, and precursor degradation were important sources of PFAA pollution in surface water. Organic carbon content was a major factor influencing PFAA distribution in sediment. These results provide a theoretical basis for revealing the regional transport and fate of PFAAs, and are also important prerequisites for effectively protecting the freshwater resource and aquatic environment of the Qinghai-Tibetan Plateau.