Background The middle and lower reaches of the Yangtze River plain produce the second highest amount of wheat in China; however, waterlogging is an important environmental factor that substantially affects the yield production of wheat (Triticum aestivum L.) in this region. Methods In this study, seven treatments were implemented, including no waterlogging and exogenous 6-benzylaminopurine (6-BA) as a control (CK); waterlogging at booting (BW), anthesis (AW) and 15 days after anthesis (DAA, FW); and spraying 6-BA before waterlogging at booting (BW-6BA), anthesis (AW-6BA) and 15 DAA (FW-6BA), to determine the ability of 6-BA to alleviate the harmful impact of waterlogging on aboveground biomass production and grain yield. The widely cultivated wheat cultivar “Zhengmai 9023” was used. Results The results showed that more than 190.0 mm of rainfall, which accounted for approximately 45.0% of the precipitation over the whole wheat growing season, was distributed after the booting stage (April and May). In all waterlogged treatments, the photosynthetic rate, aboveground biomass and grain yield decreased, but the differences between the CK and the FW treatment were not significant. The grain yield decreased by 18.38%, 41.79% and 5.67% in the BW, AW and FW treatments, respectively. Spraying 6-BA before waterlogging enhanced the root activities after anthesis and then decreased the malondialdehyde concentrations of the flag leaves and the third leaf, increased the photosynthetic rate of the flag leaves and enhanced aboveground biomass and grain yield. Among the increments between the treatments, the increments between the BW and BW-6BA treatments were the largest, but between the FW and FW-6BA were smallest. In comparison to the other waterlogging treatments, the grain yields from the FW and FW-6BA treatments were significantly higher because of the higher kernel numbers per spike. The results indicated that waterlogging after the booting stage restrained the dry matter production of winter wheat, but spraying 6-BA before waterlogging slowed the plant senescence rate and reduced grain yield loss.

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