In our study, the effects of water stress on photosynthesis and photosynthetic electron transport chain (PETC) were studied through several ways including monitoring the change of gas exchange parameters, modulated chlorophyll fluorescence, rapid fluorescence induction kinetics, reactive oxygen species, antioxidant enzymes activities and D1 protein in apple leaves. Our results showed when the leaf water potential ( ) was above -1.5MPa, the stomatal limitation should be the main reason for the drop of photosynthesis. In this period, , , , and all showed a strong positive correlation with leaf water potential. So do modulated chlorophyll fluorescence parameters related to photosynthetic biochemistry activity including F /F , Φ , q , and q as water leaf potential gradually decreased. On the contrary, in this period, NPQ and kept going up, which expresses an attempt to dissipate excess energy to avoid its damage to plants. When is below -1.5MPa, continued to decrease linearly while increased and a 'V' model presented the correlation between and by polynomial regression. It implied in this period the drop in photosynthesis activity might be caused by non-stomatal limitation other than stomatal limitation. F /F , Φ , qP, and qL in apple leaves treated with water stress were much lower than that in control while NPQ and started to go down. It demonstrated the excess energy might exceed the tolerant ability of apple leaves. Consistent with changes of these parameters, excess energy led to an increase in the production of reactive oxygen species (ROS) including H O and O Although the activities of antioxidant enzymes like catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) increased dramatically and ascorbate peroxidase (APX) decreased in apple leaves with drought stress, it was not still sufficient to scavenge ROS. Consequently, the accumulation of ROS triggered a reduction of D1 protein net content, a core protein in PSII reaction center. As D1 was responsible for the photosynthetic electron transport from Q to Q , the capacity of PETC between Q to Q was considerably down-regulated. The decline of photosynthesis and activity of PETC might result in the shortage of ATP and limitation the regeneration of RuBP ( ), a key enzyme in CO assimilation. They were all non-stomatal factors and together contributed to the decreased CO assimilation under severe water stress.