Plant growth depends on soil and water environment of root and atmospheric environment of canopy. With the synergistic effect of environmental factors, it can affect the process of plant energy transportation, material interchange, and physiological accommodation. Aiming at two different micro-environments under flooding and drought condition in paddy field, this article conducted research on the net photosynthetic rate (P_n) change law under water level regulation, and the relationship between P_n and soil and water environment and atmospheric environmental factors. Results showed that P_n descended in all growth stages under flooding or drought treatment. The descending range for lower leakage amount (2 mm/d) was slightly higher than that for higher leakage amount (4 mm/d), and it was slightly higher for heavy drought (-600 mm) with the comparison to light drought (-400 mm). P_n exhibited an impact of quadric relationship on photosynthetic active radiation (PAR) and CO₂ concentration (C_i) – both in the morning and in the afternoon, while it exhibited an impact of quadric relationship on air temperature (T_a) in the morning, and a linear relationship in the afternoon. It showed no obvious relationship on relative humidity (RH) and vapor pressure deficit (VPD). With the comparison of two photosynthetic light response models under water-level regulation, it illustrated the flooding and drought conditions that resulted in P_n decreasing according to the light suppression effect, while it showed the physiological compensation effect after rewatering. Additionally, the new photosyntheticlight response model fit better on the photosynthetic-light response curve than the non-rectangular hyperbolic model.