The altitude effect of isotopes in precipitation is not as significant on the leeward side of a mountain as it is on the windward side, which makes it difficult to use isotopes at leeward sites, especially if estimating elevation of groundwater recharge or reconstructing paleoelevations. Samples of precipitation were taken at three stations with different elevations-2,306-3,243 m above mean sea level (asl)-on the leeward side of the Meili Snow Mountains on the southeastern Tibetan Plateau from August 2017 to July 2018. The isotope vs. altitude gradients were calculated based on two adjacent stations at the daily, monthly, and annual scales. Most of the gradients are beyond the global ranges of -0.5 to -0.1 parts per thousand per 100 m for delta O-18 and -5 to -1 parts per thousand per 100 m for delta H-2, and some of the gradients are even positive. Local processes of sub-cloud evaporation and mixing with recycled moisture are identified for the ambiguous altitude effect, while regional atmospheric circulation processes dominate the major patterns of stable isotope variation at the three stations. The groundwater recharge elevation is estimated to be in a very large range, 2,562-6,321 m asl, which could be caused by the differences in isotope vs. altitude gradient in the studied catchments. Considering the complex atmospheric processes affecting precipitation isotopes, sampling of event-based/monthly precipitation at more than two altitudes for at least one complete hydrological year is a minimum requirement to establish a reasonable isotope vs. altitude gradient.