In this study, we evaluated the photosynthetic performance of Zanthoxylum armatum seedlings to test the tolerance to reoxygenation after waterlogging. The experiment included a control group without waterlogging (NW) and three reoxygenation groups with reoxygenation after 1 day (WR1), 2 days (WR2) and 3 days (WR3). Seedlings were pretreated with concentrations of 0, 200 and 400 µmol L-1 of ethylene. The results showed that reoxygenation after waterlogging for 1–3 days decreased photosynthetic pigments content, enzymes activity, stomatal conductance (Gs), net photosynthetic rate (Pn), transpiration rate (Tr) and water-use efficiency (WUE). However, pretreatment with ethylene increased photosynthetic pigments content, enzymes activity and gas exchange parameters under both NW and WR3 treatments. The chlorophyll fluorescence results showed that the maximum quantum yield of PSII (Fv/Fm) and actual photochemical efficiency of PSII (FPSII) remained no significant changes under the NW and WR1 treatments, while they were significantly reduced with an increase in waterlogging days followed by reoxygenation under WR2 and WR3 treatments. Exogenous ethylene inhibited Fv/Fm and the non-photochemical quenching coefficient (NPQ), while enhanced FPSII and electron transfer efficiency (ETR) under WR2 treatments. Moreover, the accumulation of exogenous ethylene reduced photosynthetic ability. These findings provide insights into the role of ethylene in enhancing the tolerance of Z. armatum to reoxygenation stress, which could help mitigate the impact of continued climate change.