Understanding the stoichiometric characteristics of plants to a substrate shift is a key step in the use of a stoichiometric framework to predict ecosystem responses to environmental change. However, the response and mechanism of stoichiometry to a substrate shift in facultative epiphytes remains unknown. The foliar stoichiometric (N, P, K, Ca, Mg, S, Mn, Na, and Fe concentrations) and isotopic characteristics (delta C-13 and delta N-15) of nine facultative epiphyte species in Xishuangbanna karst forest in southwest China were determined. The stoichiometry and isotopy were compared between the epiphytic and lithophytic individuals in the facultative epiphytes, and the possible causes of changes in elemental concentrations to substrate shifts were studied. We found that the lithophytes were enriched in delta N-15 and Ca, but depleted in elements such as Fe, K, and Mn compared with the epiphytes. The delta N-15 was positively correlated with P, N, S, and K, while the delta C-13 was negatively correlated with delta N-15, P, N, S, and Fe. Following a principal component analysis (PCA), the first axis loaded organically bound elements (P, N, and S), while the second axis loaded non-organically bound elements (Fe, Mn, and K). The variances of non-organically bound elements were mostly affected by the substrate-related factors than organically bound elements. These results revealed that the substrate factor has a strong partitioning effect on elements such as K, Ca, Fe, Mn, and delta N-15. The differences of element concentration and isotopy between the two ecotypes suggested stoichiometric and isotopic flexibility, which enabled facultative epiphytes to exploit rock and bark interchangeably.