A field experiment was performed to study the effects of waterlogging on the leaf mesophyll cell ultrastructure, chlorophyll content, gas exchange parameters, chlorophyll fluorescence, and malondialdehyde (MDA) content of summer maize (Zea mays L.) hybrids Denghai605 (DH605) and Zhengdan958 (ZD958). The waterlogging treatments were implemented for different durations (3 and 6 days) at the third leaf stage (V3), the sixth leaf stage (V6), and the 10th day after the tasseling stage (10VT). Leaf area index (LAI), chlorophyll content, photosynthetic rate (Pn), and actual photochemical efficiency (ΦPSII) were reduced after waterlogging, indicating that waterlogging significantly decreased photosynthetic capacity. The chloroplast shapes changed from long and oval to elliptical or circular after waterlogging. In addition, the internal structures of chloroplasts were degenerated after waterlogging. After waterlogging for 6 d at V3, the number of grana and grana lamellae of the third expanded leaf in DH605 were decreased by 26.83% and 55.95%, respectively, compared to the control (CK). Those in ZD958 were reduced by 30.08% and 31.94%, respectively. Waterlogging increased MDA content in both hybrids, suggesting an impact of waterlogging on membrane integrity and thus membrane deterioration. Waterlogging also damaged the biological membrane structure and mitochondria. Our results indicated that the physiological reactions to waterlogging were closely related to lower LAI, chlorophyll content, and Pn and to the destruction of chloroplast ultrastructure. These negative effects resulted in the decrease of grain yield in response to waterlogging. Summer maize was the most susceptible to damage when waterlogging occurred at V3, followed by V6 and 10VT, with damage increasing in the wake of waterlogging duration increasing.