Alpine shrub Quercus aquifolioides was selected to study the effects of shrub canopy on throughfall and phreatic water by analyzing the isotopic time series of precipitation, canopy throughfall and phreatic water and examining correlations among these series in Wolong Nature Reserve, Western China. Based on analysis of precipitation data in 2003, the local meteoric water line during the rainy season was dD ¼ 8.and the primary precipitation moisture in this region originated from the Pacific Ocean in the summer. Stable isotope analysis showed that the main supply of throughfall and phreatic water was from precipitation, and the shrub canopy has an important effect on the processes of rainwater transmuted into throughfall and phreatic water. Moreover, the differences of dD and d 18 O values between rainwater and throughfall were relevant to rainfall. Due to interception of the shrub canopy, there had a response hysteresis of phreatic water to the various rainfall events, which was mostly 2 days, except that this hysteresis was 1 day when rainfall was >15 mm/day.