Wheat (Triticum aestivum L.) plants were subjected to combined waterlogging and shading (WS) at 0–7, 8–15, 16–23 and 24–31 days after anthesis (DAA). WS at 0–7, 8–15, 16–23 and 24–31 DAA caused a yield loss of 17.18%, 14.98%, 7.93% and 7.05%, respectively. These losses were related to reductions in post-anthesis photoassimilate accumulation and 1000-kernel weight. WS reduced net photosynthetic rate (Pn), the maximum efficiency of PSII photochemistry under dark adaptation, actual photosynthetic efficiency and the photochemical quenching coefficient, but increased the quantum yield of quenching. WS caused enhanced concentrations of malondialdehyde and H2O2, and an increased superoxide anion release. Superoxide dismutase and catalase activity were stimulated at 4 days after the onset of WS at 0–7 and 8–15 DAA, but decreased at 8 days after the onset of WS at 0–7, 8–15 and 16–23 DAA. Ascorbate peroxidase, glutathione reductase, dehydroascorbate reductase and monodehydroascorbate reductase activity increased during 0–8 days after the onset of WS at 0–7, 8–15 and 16–23 DAA. At 16–24 DAA, Pn, the level of reactive oxygen species and activity of the antioxidative enzymes fully recovered in plants subjected to WS at 0–7 DAA, but only partially recovered under WS at 8–15 DAA. Expression of the photosythesis-responsive genes RcaB and Cab, and the antioxidative enzyme-related genes Mn-SOD, Cu/Zn-SOD, CAT and GR were consistent with the performance of Pn and the activity of the antioxidative enzymes.