Abstract: In order to reveal the seedling morphological characters under different temperature conditions and heat resistance of the molecular genetic basis, this study with 9B in indica and japonica M494 recombinant inbred lines derived from hybridization（Recombinant inbred line, RIL） group as the experimental material, combined with high density SNP map, QTL analysis was performed on plant height, root length, above ground dry weight, underground dry weight, above ground fresh weight, underground fresh weight and dry and dead leaf length of Oryza sativa L. after high temperature treatment under two temperature conditions. The results showed that there were obvious differences in heat resistance of RIL population at the seedling stage under two temperature conditions. A total of 28 QTLs related to morphological traits and heat resistance at seedling stage were detected, which were distributed on the 1 st, 2 nd, 3 rd, 4 th, 7 th, 8 th and 10 th chromatics, and the explicable phenotypic tribute rates ranged from 3.26% to 34.10%. Among them, in the Chunk343-351 interval of No.3 dye body, there were major QTL clusters that controlled dry and dead leaf length, plant height, above ground fresh weight, underground fresh weight, above ground dry weight and underground dry weight at the same time under two temperature conditions. There was a QTL in Chunk338-343 of chromosome 3 that controlled root length under high temperature conditions. A new QTL locus was detected in the Chunk796-803 region of chromosome 8, which regulated both above-ground fresh weight and subsurface fresh weight under high temperature conditions.