The purpose of this study is to explore the role of mitochondrial alternative oxidase (AOX) in photoprotection in apple leaves under water stress. After treated with salicylhydroxamic acid (SHAM) to inhibit the AOX pathway, we studied the effects of AOX pathway on photoprotection in Malus hupehensis detached leaves under water stress by simultaneously analyzing chlorophyll a fluorescence transient and light absorbance at 820 nm. The results indicated that water stress induced the upregulation of AOX activity. The inhibition of AOX pathway caused more severe photoinhibition. Under water stress, maximum quantum yield of primary PSⅡ photochemistry (TRo/ABS) and PSⅡ trapped electron being transferred from Q_A to Q_B (ETo/TRo) decreased, average absorbed photon flux per PSⅡ reaction center (ABS/RC) increased, while the maximum PSⅠ redox acitity(ΔI/I_o) was not affected. After treated with SHAM to inhibit the AOX pathway, ABS/RC markedly increased, TRo/ABS, ETo/TRo as well as ΔI/I_o significantly decreased. It was indicated that under water stress the inhibition of AOX pathway caused more severe photoinhibition, especially to the PSⅠ. Generally, the results demonstrate that the AOX pathway played an important role in the photoprotection in M. hupehensis leaves under water stress, particularly in the photoprotection of PSⅠ.