Rice is a moderately salt-sensitive crop, and its yield will be severely affected when grown in saline soils. Exploring salt-tolerance related genes and clarify the molecular mechanism of salt tolerance are important for the breeding of salt-tolerant rice varieties and the efficient utilization of saline soils. Previously, our laboratory created a strong salt-tolerant chromosome segment substitution line CSSL91 using Dongxiang common wild rice and Nipponbare as the parents, and its salt tolerance was comparable to that of Pokkali. In this study, the F2:3 population constructed from CSSL91 and Nipponbare was used as experimental material. With salt tolerance grade and seedling survival rate as indicators, five salt tolerance-related QTLs were detected, distributed on chromosomes 4, 9, and 10, with LOD values ranging from 2.95 to 3.97 and phenotypic contribution rates ranging from 9.83% to 18.48%. Among them, the salt tolerance grade QTL qST4 had the highest phenotypic variation contribution of 18.48%, localized between markers DX-C4-1 and DX-S4-16 on chromosome 4, and the locus could be detected by both linkage marker analysis and BSA analysis. QTLs qST4-1 for salt tolerance grade and qSSR4 for seedling survival rate were both located between markers DX-C4-12 and DX-C4-13 on chromosome 4, with LOD values of 3.36 and 3.92, and phenotypic contribution rates of 13.97% and 9.49%, respectively. In addition, two salt tolerance grade QTLs, qST9 and qST10, were located on chromosomes 9 and 10, respectively. The qST4-1/qSSR4 and qST10 are the newly localized salt tolerance-related QTLs in this study. The results of this study will lay the foundation for the cloning of salt tolerance-related genes and the improvement of rice salt tolerance varieties by molecular marker assisted selection.