Frequent waterlogging events have severely constrained wheat production in the middle and lower reaches of the Yangtze River, China (YR). Understanding the effects of waterlogging on agronomic traits and grain yield in historic wheat cultivars can help establish strategies for stable- and high-yield breeding programs. We conducted a two-year field experiment using 10 winter wheat cultivars that were released and widely planted in YR from 1967 to 2010. Ten days of waterlogging were imposed on plants beginning at stem elongation (Zadoks growth stage, GS33). Grain yield was improved with the year of cultivar release, gaining 53 kg ha−1 yr−1 (0.6% yr−1) under normal watering condition and 35 kg ha−1 yr−1 (0.51% yr-1) under waterlogging treatment from 1967 to 2010, showing that waterlogging tolerance declined with cultivar improvement. Yield improvement was primarily due to the synergistic development of kernels per spike and 1000-kernel weight, as well as the increased harvest index from the 1960s to 1990s and the increased total biomass from the 1990s to 2000s. Furthermore, genetic improvement significantly increased post-anthesis biomass, leaf area at milk-ripe (GS75), and net photosynthetic rate in flag leaf. Due to waterlogging, kernels per spike, sing-spike yield, total biomass, post-anthesis biomass, leaf area at milk-ripe decreased more with the year of cultivar release, but we did not find a significant reduction in spikes per m2, 1000-kernel weight, and harvest index across cultivars. Grain yield and single-spike yield were significantly and positively correlated with leaf area at milk-ripe, as well as net photosynthetic rate in flag leaf. However, their reductions were only significantly correlated with the reduction in leaf area. Moreover, waterlogging did not significantly affect flag leaf area. This study suggests that improving the photosynthetic capacity of flag leaf will assist in the selection of new wheat varieties with waterlogging-tolerance and high-yields. Further studies are required to investigate the responses of wheat canopy architecture and photosynthesis to waterlogging and their functions for crop yield.