The groundwater in shallow loess aquifers in high mountain-hills in the western Loess Plateau in China is almost the sole water resource for local residents. However, the question about how the loess groundwater naturally circulates in these high mountain-hills, characterized by low precipitation and high potential evaporation, remains unclear. The objectives of this study are to evaluate the application of hydrogen and oxygen isotopes to (1) examine temporal variations of the isotopic composition of precipitation and shallow groundwater and (2) uncover the mechanism of groundwater recharge in high mountain-hills. Results from 2 years of monitoring data show a difference in the stable isotopes for groundwater and local precipitation between the winter and summer periods. Similar to precipitation, stable isotopes in groundwater are observed to be depleted in winter and enriched in summer, particularly in oxygen isotope. A prominent characteristic is that H and O isotopes of groundwater show a very clear response to strong precipitation in the rainy season in 2013. The results highlight that local precipitation is the likely recharge source for groundwater in shallow loess aquifers. Annual recharge from local precipitation maintains the groundwater resource in the shallower loess aquifer. The mechanisms governing shallow loess groundwater recharge in high mountain-hills were evaluated. In addition to possible vertical slow percolation of soil water through the unsaturated zone, rapid groundwater recharge mechanisms have been identified as temporal preferential infiltration through sinkholes, slip surface or landslide surface and through the interface of loess layer and palaeo-soils. Most groundwater can be recharged after a heavy rainy season.