The high germination rate at relatively low temperature (HGR-LT) is one of the main factors restricting the development of seedling of direct-seeding rice. It is very important to study the genetic and molecular mechanism of HGR-LT for the breeding of fine varieties in direct-seeding rice. In this research, 140 backcross inbred lines (BILs), derived from a japonica super rice shennong265（SN265）as the recurrent parent and the Dongxiang wild rice ( Oryza wild rice Griff. ) as the donor parent, were used to detect the QTLs for HGR-LT. Total of 10 lines, with HGR-LT and good agronomic traits were selected according to the comprehensive performance under low temperature, providing the basic materials for the improvement of HGR-LT in super rice, SN265. It was found that 4 markers linkage to cold tolerance genes on chromosome 2 (RM324 and RM166), 5 (RM534) and 9 (RM257) with BSA (Bulked Segregate Analysis)．Meanwhile, a total of 15 QTLs were detected on chromosomes 1, 2, 4, 5, 6, 7 and 11 by linkage map, which explained 11.48% ~17.72% of the phenotypic variance. The 2 of these 15 QTLs, qGP-2-1 and qGP-2-4 on chromosome 2 were the same with the RM324 and RM166 obtained through the BSA selection, which could be used for molecular marker assisted selection of HGR-LT.