A population of recombinant inbred lines (RILs, F2:9), derived from a cross between IR26 (Oryza sativa subsp. indica) and Jiucaiqing (Oryza sativa subsp. japonica), was used to identify seed germination ability of rice under 100 mmol/L NaCl for 10 days. Six germination traits including imbibition rate, germination rate, germination index, root length, shoot length and vigor index were investigated. A mixed major gene and polygene inheritance model was applied to conduct genetic analysis for germination ability. Significant differences were detected in all the germination traits under salt stress among RILs in rice, and the early germination stage (0-5 days) might be the salt sensitive stage. The frequency distributions of the germination traits under salt stress in the RIL population showed continuous segregation, suggesting that they were quantitative traits controlled by several genes. The germination traits under salt stress were regulated by two or three major genes plus polygene, and mainly dominated by major genes with high heritability values, accounting for 12.5%-99.0% of the total phenotypic variation. Each trait was controlled by the specific genetic model: imbibition rate was controlled by two major genes, germination index and vigor index by two major genes plus polygene, germination rate and shoot length by three major genes plus polygene, and root length by two major genes or two major genes plus polygene.