Abstract: Background Mountains in Beijing are in an ecologically fragile area with seasonal drought; therefore, study of water source of typical tree species before and after the rain in arid areas is of great significance. Methods By taking Pinus tabulaeformis and Platycladus orientalis in mountains in Beijing as subject, we employed the hydrogen and oxygen isotope technique and measured the isotopic composition in branches of trees, soil, groundwater and rainfall in order to clarify their water source before and after the rain. Results The results showed that the soil moisture content and the isotope of the two species showed a vertical change. P. tabuliformis and P. orientalis forest soil were different in soil moisture content before rainfall. Soil moisture content in Platycladus orientalis layers was lower than that in Pinus tabulaeformis. The average soil moisture content was 7.44% and 2.17%, respectively. After the rainfall, soil moisture content in the stands of two typical species were higher than before, the average soil moisture content in the P. orientalis stand increased by 46.1% compared to that before rainfall, while it increased by 38.7% for P. tabuliformis. The intense evaporation of surface soil water caused the isotope fractionation and enrichment heavy isotopes. Decreasing with soil depth, soil water D in P. tabuliformis and P. orientalis stands showed a tendency to increase, and the heavy isotope was enriched. Different plant species had different water sources in the same season, and the same plant species had different water sources before and after the rain, showing an adaptation to their habitats. P. tabuliformis had fewer roots in urface soil, but still absorbed a high amount of topsoil water before rainfall, with a utilization rate of 36.0%; in order to obtain a stable water supply, P. tabuliformis used the developed deep roots to absorb underground water with a utilization rate of 38% and 58.2%, before and after rain, respectively. P. orientalis used deep soil water to maintain normal physiological activities, and the utilization rate was 71.2%. The lateral root in the surface layer soil of 0 -20 cm was sensitive to rainfall, and P. orientalis mainly used surface soil moisture with a utilization rate of 71.6%. Conclusions Our results have great significance for artificial afforestation, tree species configuration and alleviation of the water resource shortage in arid and semi-arid areas.