Rice is highly sensitive to salinity stress during the seedling establishment phase. Salt stress is widely occurring in cultivated areas and severely affects seed germination ability and seedling establishment, which may result in a complete crop failure. The objective of the present study is to identify quantitative trait loci (QTLs) related to salt tolerance of the germination and seedling stages in a rice backcross inbred line (BIL) population that was derived from a backcross of an Africa rice ACC9 as donor and indica cultivar Zhenshan97 (ZS97) as the recurrent parent. Under salt stress, ACC9 exhibited a higher germination percentage, but more repressed seedling growth than ZS97. Using the BIL population, 23 loci for germination parameters were detected at the germination stage and 46 loci were identified for several morphological and physiological parameters at the seedling stage. Among them, nine and 33 loci with the ACC9 alleles increased salt tolerance at the germination and seedling stages, respectively. Moreover, several major QTLs were found to be co-localized in the same or overlapping regions of previously reported genes for salt stress. These major loci will facilitate improving salt-tolerance rice in genome-breeding programs.