The quantitative trait loci (QTLs) for low-temperature vigor of germination (LVG) with a germination period of 7 d, 11 d, 14 d, and 17 d at 14 degrees C was identified using F(2:3) population, which included 200 individuals and lines derived from a cross of indica and japonica "Milyang 23/Jileng 1" with microsatellite markers. The correlation coefficient between LVG and other cold tolerance traits was analyzed. LVG and the cold response index for vigor of germination (CIVG) detected when the germination period was 7 d showed a continuous distribution, which was partial to lower LVG and lower CIVG in F(3) lines. LVG and CIVG detected when the germination periods were 11 d, 14 d, and 17 d showed a continuous distribution near normal, which were quantitative traits controlled by multiple genes. LVG detected when the germination period was 14 d was more correlated with other cold tolerance traits than LVG detected when the germination periods were 7 d, 11 d, and 17 d, which was significantly associated with cold tolerance during the bud bursting period, the seedling stage, the booting stage, and the growing ability under cold conditions. qLVG2 located in RM29-RM262 on chromosome 2, qLVG7-2 and qCIVG7-2 located in RM336-RM118 on chromosome 7 were detected when the germination periods were 11 d, 14 d, and 17 d. qCIVG2 located in RM29-RM262 on chromosome 2 was detected when the germination periods were 11 d and 14 d. The variation is due to the observed phenotypic variation by the above QTLs, which was increased following the germination. The variation of qLVG2 related to LVG was increased from 6.9% to 14.2%. The variation of qLVG7-2 associated with LVG was increased from 9.9% to 11.2%. The variation of qCIVG2 correlated with CIVG was increased from 6.3% to 9.0%. The variation of qCIVG7-2 associated with CIVG was increased from 8.3% to 12.9%. These QTL alleles were obtained from the tolerant parent Jileng 1, and the gene action was most likely to be partially dominant.