Nowadays, groundwater quality has deteriorated because of intensive human activities. It is important to accurately identify the pollution source for controlling the deterioration of groundwater quality. However, the accuracy of the current source analysis method needs to be improved. In this study, we combined hydrochemical method, isotope tracing technique and PMF model, for the first time, to trace the source of groundwater pollution in Beichuan River basin, Qinghai Province, China. According to the results, there were 35.8% of Fe, 34.1% of total hardness, 24.3% of SO42− and 8.09% of NO3− samples exceeded the Grade III standards for Groundwater quality in China, which indicated that the groundwater in the study area has been significantly affected by human activities. Hydrochemical method suggested that the chemical component originated from rock weathering, cation exchange and mineral dissolution. Based on isotope tracing technique (δ15N–NO3-, δ18O–NO3-, δ34S–SO42− and δ18O–SO42−), the primary sources of nitrate and sulfate in groundwater were soil nitrogen and oxidation of sulfide minerals in the forest area, domestic sewage and oxidation of sulfide minerals in the urban and industrial area, and mixed sources in the village and agricultural area. Finally, the pollution source of groundwater was distinguished by combining the PMF model, isotope tracing technique and hydrochemical method. Results showed that the main pollutant of groundwater is domestic sewage in the urban, village and industrial area. The contribution rates to groundwater pollution were 60.7%, 60.8% and 57.8%, respectively. However, in the forest and agricultural area, the main source changed to water-rock interaction and chemical fertilizer, and the contribution rates to groundwater quality were 53.5% and 61.0%, respectively. Our results suggested that the coupling tracing methodology can improve the accuracy of source resolution in the water environment and it can be applied to other areas of the world.