To screen new rice storage tolerance germplasm, seed of one recombinant inbred lines (RILs) population that had been in natural storage for 4 years and derived from the cross between japonica cultivar ‘Mowanggu’ (MGW) and indica rice ‘CO39’ was used to analyze the germination phenotype of seed from the population and to map QTLs responsible for seed storage tolerance trait by composite interval mapping. The results showed that, the phenotype of germination rate, germination potential, and germination index of 67% lines from the 101 RIL lines was declined to 0. The value of the 3 traits for other lines ranged from 0-82.67%, 0-46.00% and 0-6.48 respectively. Only one line still keeps a high germination rate of 82.67%. QTL mapping yielded 3 QTLs responsible for germination traits, namely qGP7, qGE7 and qGI7. Among them, qGR7 was mapped in the interval of SSR marker RM6344 and RM5720 with a distance of 18.43 cM, qGP7 and qGI7 located in the same interval between SSR maker RM5672 and RM8261 with a distance of 35.74 cM. The LOD values of 3 QTLs ranged from 2.52-2.56, of which the phenotypic contribution rate was 12.02%-12.22%.