Wheat production is seriously influenced by extreme hot weather, which has attracted increasing attention. It is important to compare wheat responses to heat at seedling and reproductive stages, to explore the potential relationship between the performances at different growing stages and the possibility of early selection to accelerate heat tolerance breeding. In this study, forty wheat genotypes were screened under heat stress at both seedling and adult stages. It was found that root lengths at seedling stage were severely reduced by heat stress with significant variations among wheat genotypes. Heat-tolerant genotypes at seedling stage showed less root length decrease than susceptible ones. Wheat genotypes tolerant at seedling stage showed higher yield at adult stage after heat treatment. The performances of wheat genotypes screened under heat stress at seedling and adult stages were ranked by seedling damage index and adult damage index. A significant positive relationship was found between heat tolerance at seedling stage and at adult stage (r = 0.6930), suggesting a similar tolerant/susceptible mechanism at different plant growth stages and the possibility of early selection at seedling stage for breeding heat tolerance. Extremely tolerant and susceptible genotypes with consistent performances at seedling and adult stages were genetically compared and associated SNP markers and linked candidate genes were identified.