In southern China, rice (Oryza sativa L.) grains are prone to field pre-harvest sprouting (PHS) due to high temperature and humid weather conditions, which seriously affects the yield, quality and storage of rice. Moderate seed dormancy prevents the adverse effects of the unfavorable environment and helps reduce or avoid PHS. Therefore, genetic studies of seed dormancy and breeding PHS-resistant varieties, are extremely important for rice production and development of seed industry. In this study, we used the indica cultivar ‘93-11’ as the recipient and recurrent parent, and Chaling common wild rice (CLCW) of O. rufipogon Griff. as the donor parent to develop an advanced backcross introgression population consisting of 812 lines. We assessed the seed dormancy of the population, and found five individual plants displaying strong dormancy with the germination rate ranging from 10.0% to 36.5%, while the control and recurrent parent ‘93-11’ had the germination rate of 89.5%. The germination rate of the selfed lines derived from the five strong-dormancy plants ranged from 3.1% to 17.4%. The plants with extremely strong seed dormancy selected from each of 3 selfed lines were crossed with ‘93-11’ to develop the F2 population. By combining the bulked segregant analysis (BSA) and 56K SNP chip data, 8 QTLs were detected, distributed on chromosomes 3, 5, 6, and10. This study will facilitate further map-based cloning of these QTLs and breeding PHS-resistant rice varieties.