To map the cold-tolerant QTL in rice, the recombinant inbred lines (RILs) population derived from the cross between ‘Wufeng B’ and ‘Changhui T025’, the parents of double-cropping super rice ‘Wufengyou T025’, were used as the materials. The survival rate, root number, root length and bud length at young seedling stage treated at low temperature of 10℃ were determined. Three QTL, qRL1, qRL2, and qBL6 controlling the cold tolerance of rice at seedling stage, were detected by QTL Icimapping v4.2 software. These QTL were identified on chromosome 1, 2 and 6, respectively, their LOD values were 2.98, 2.51 and 5.26, respectively, and the phenotypic variation explained by these QTL were 10.54%, 8.67% and 14.04%, respectively, and the positive alleles of the three QTL were all from ‘Changhui T025’. These QTL were mapped at an interval of 6.75k-40.05kb on Nipponbare genome, which laid the foundation for the improvement of indica cold tolerance at young seedling stage by using these favorable QTL via marker-assisted selection. Furthermore, 13 pairs of epistatic interaction QTL were detected on all 12 chromosomes, and the epistatic interaction between chromosome 3 and chromosome 8 accounted for 21.77% of the phenotypic variation. The results indicate that the epistatic interaction effect plays an important role in rice cold tolerance at young seedling stage.