Alternate bearing (AB) trees, including Malus prunifolia, are characterized by alternating cycles of heavy (ON tree) and low (OFF tree) fruit loads. The mechanisms regulating the AB phenomenon have not been fully characterized. We completed an iTRAQ-based investigation of M. prunifolia to identify the proteome and metabolic differences between the leaves of ON and OFF trees. We identified 667 differentially expressed proteins, and they influenced multiple biochemical pathways, including photosynthesis, carbohydrate metabolism, glycolysis, protein processing, redox activities, and secondary metabolism. Bioinformatics analyses indicated photosynthesis was the most significant biological process affecting the AB. We observed that 47 photosynthetic proteins affecting photosystem I and II reaction centers, cytochrome b6/f complex, electron transport, and light-harvesting chlorophyll were less abundant in ON tree leaves than in OFF tree leaves. Additionally, physiological analyses validated the potential metabolic activities. Nitrogen and phosphorus contents were significantly higher in ON tree leaves, while potassium levels were lower. Starch content, ZR, GA4+7 levels, and flower control gene expression levels (i.e., MdFT1, MdLFY, MdAP1, and MdSPL9) were lower in ON tree leaves than in OFF tree leaves, suggesting they affected the AB phenotype. Our findings help further investigate on the photosynthesis as well as other processes in AB. Those identified DEPs and important biological processes can be useful theoretical basis and provide new insights into the molecular mechanisms regulating AB in perennial woody plants.