Abstract: Following a twofactor split plot design, two popular varieties (Neimai836 and Chuanmai104) were used to study the effects of waterlogging at four growth stages (seedling, jointing, booting and anthesis) on wheat growth and yield formation during two growing seasons (2011-2012 and 2012-2013). The resulted showed that the greatest yield penalty occurred when waterlogging happened at the seedling stage (10%-15% decrease), and it was alleviated when waterlogging happened at the other stages. Waterlogging during the seedling stage significantly reduced SPAD of 2nd-6th leaves, tillers and spike number per plant, productive ears, dry matter accumulation after flowering and dry matter at maturity. Waterlogging during the jointing stage decreased SPAD of 4th-7th leaves, and waterlogging  during the booting stage reduced the SPAD of top 2nd, 3rd, 4th leaves. Waterlogging during the jointing and booting stages reduced the SPAD of flag leaf, the rate of grain filling during the gradual increase stage, the average filling rate and the 1000grain mass. Waterlogging during the flowering stage produced limited change in yield. Therefore, waterlogging during the seedling stage was identified to have the most critical influence on  wheat production under wheat/rice cropping rotations in Sichuan Province.