Cold sensitivity has been shown to vary and the cold tolerance from vegetative to reproductive stage appears to be independent during the life cycle. In the current study, cold tolerance under high elevation rice growing area were evaluated using F4 generation of 181 lines derived from Gayabyeo*2/Chhamrong. Five main-effect QTLs related to days to heading, panicle exertion and spikelet fertility were identified. The QTL qDH-3 on chromosome 3 showed the peak LOD score of 6.3, explaining up to 16.5% of phenotypic variation with additive effect of -2.6. Moreover, the QTL qPE-3 and qSF-3 on chromosome 3 were coincided with the QTL qDH-3 showing an opposite allele effects. Thus, the region harboring marker RM523-RM14281 could be helpful for the selection of cold tolerance genotypes in marker assisted selection(MAS) of rice breeding program.