Within this study, a QTL mapping of salt tolerance was conducted by using a population of chromosome segment substitution lines (CSSLs), which were generated from common wild rice as donor parent and cultivated rice (9311) as receive parent. Genotyping for CSSLs were performed with types of markers (SSR, InDel and genotyping-by-sequencing markers). The phenotypic datasets were assessed by systemically evaluating the salt tolerance at different growth periods. As a result, two QTLs at germination stage and 13 QTLs at seedling stage were obtained. Among QTLs, qSSR5.1 and qSSG5.1 were found at the same locus, which synergistically contributed to the seedling survival rate (6.36%) and salt tolerance grade (8.13%). Within the target interval, one candidate gene OsDi19-1 which associated with abiotic stress was found. Sequence alignment showed an obvious sequence variation between 9311 and wild rice in the promoter region of OsDi19-1. Notably, the line CSSL72 showed a higher germination rate, while CSSL23 and CSSL153 exhibited higher seedling rates. A down-regulation on gene expression was observed in CSSL23 and CSSL153, if relative to 9311 under salt treatment. Taken together, our data indicated that OsDi19-1 from wild rice might contribute to the salt tolerance, and these elite lines might become useful in future rice salt tolerance breeding.