Leaf photosynthesis is pivotal for the synthesis of carbohydrates; however, the growth and development of horticultural crops are more closely related to canopy photosynthetic capacity. Measurements of canopy photosynthesis allow a better evaluation of the fruit tree performance at the canopy scale. Therefore, an open chamber system to determine instantaneous canopy apparent photosynthesis (CAPi) was investigated. CAPi slightly overestimated the biomass accumulation by 5.9%, which revealed that the CAPi method is valuable for quantifying canopy photosynthesis. Further, many woody horticultural plants are usually grafted for propagation, such as apples, whereas the rootstocks always influence the canopy size and photosynthesis. In this study, the effect of dwarfing, semi-dwarfing, and vigorous apple rootstocks on canopy photosynthesis was studied. Compared to vigorous rootstock, dwarfing rootstock significantly reduced the leaf net photosynthetic rate and total leaf area by 20.8% and 53.1%, respectively, and resulted in a 59.7% reduction in CAPi. Throughout the study, CAPi was an effective method that should be considered for canopy photosynthesis measurement of horticultural crops in the future.