Soil salinization is one of the major environmental factors that restrict plant growth and development. Zeaxanthin epoxidase (ZEP) functions in ABA biosynthesis and the xanthophyll cycle and has a vital role in plant responses to various environmental stresses. It was found by quantitative real-time PCR (qRT-PCR) that responded to saline-alkali stress and showed the highest expression at 48 h of saline-alkali stress, which was 14.53-fold of 0 h. The gene was cloned from the apple rootstock begonia ( Koehne) and its protein physicochemical properties were analyzed. Subsequently, the functional characterization of (ID: 103403091) was further investigated in . The contained a complete open reading frame with a length of 1998 bp, and encoded 665 amino acids with an isoelectric point of 7.18. Phylogenetic tree analysis showed that was the most homologous and closely related to . Compared with wild-type, transgenic plants grew better under saline-alkali stress and the -OE line showed higher chlorophyll content, carotenoid content, enzyme activities (POD, SOD, CAT and APX) and K content, whereas they had lower chlorosis and Na content than the wild type (WT), which indicated that they had strong resistance to stress. The expression levels of saline-alkali stress-related genes in -OE were examined by qRT-PCR, and it was found that the improved the tolerance of to saline-alkali stress tolerance by regulating the expression of carotenoid synthesis genes (, , and ) and ABA biosynthesis genes (, and ). And the potassium-sodium ratio in the cytoplasm was increased to maintain ionic homeostasis by modulating the expression of Na transporter genes ( and ) and K transporter genes (, and ). Moreover, the expression of H-ATPase genes ( and ) was increased to reduce the oxidative damage caused by saline-alkali stress. In summary, acted as an essential role in plant resistance to saline-alkali stress, which lays the foundation for further studies on its function in apple.