Flowering crabapples are a series of precious ornamental woody plants. However, their growth and development are inhibited in the subtropical regions due to the weak photosynthesis under high-temperature environment in the summer. Chlorophyll a fluorescence transient and 2-dimensional electrophoresis (2-DE) analyses were conducted to investigate the response characteristics of photosynthesis under simulated 38 °C heat stress in leaves of Malus. ‘Prairifire’, a spring-red leaf cultivar of flowering crabapple with strong thermal adaptability. In the present study, the net photosynthetic rate (Pn) was significantly decreased during the heat shock process, which showed a similar trend to the stomatal conductance (Gs), indicating a sensitive stomatal behavior to heat stress. Moreover, an efficient reaction center in photosystem II (PSII), and a functionally intact oxygen-evolving complex (OEC) conferred strong photosynthetic adaptability under heat stress. The higher level of transketolase (TK) under 48-h heat shock treatment was considered a protective mechanism of photosynthetic apparatus. However, heat stress inhibited the functions of light harvesting complex II (LHCII), electron transport in PSII, and the levels of key enzymes in the Calvin cycle, which were considered as the reasons causing an increase in the proportion of non-stomatal restrictions.