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Frequent waterlogging near anthesis is a primary constraint for wheat production in the Yangtze River Basin, China. This study aimed to identify the critical stage for waterlogging on wheat yield and its components and identify the possible factors determining this stage. In the first experiment (E1), we evaluated three varieties and initiated a 10-day waterlogging starting at the stem elongation (S1), booting (S2), and anthesis (S3) stages. In the second experiment (E2), waterlogging was applied at the stem elongation (S1) and anthesis (S3) stages and for three durations (five, 10, and 15 days). In E1, waterlogging at S1 and S2 resulted in a lower grain yield than at S3. In the second year of E1, grain yield under waterlogging at S1 and S3 was similar but significantly lower than under waterlogging conditions at S2. Waterlogging at S1 and S2 greatly decreased the kernel number per spike and 1000-kernel weight, but waterlogging at S3 only decreased the 1000-kernel weight. Moreover, different varieties did not change the stages mostly reducing grain yield and yield components. In E2, grain yield decreased with prolonged exposure to waterlogging and was significantly lower under 15-day conditions than the five-day conditions. There was no significant interaction between the stage and duration of waterlogging. Finally, our results indicate that in yield formation, a greater reliance on kernel weight instead of the kernel number per spike can contribute to a reduction in yield loss for waterlogging at S1 and S2. This study, therefore, indicates that the stem elongation stage is the most affected by waterlogging. [ABSTRACT FROM AUTHOR]