Abstract: The aging of soybean seeds under long-term storage conditions leads to the reduction of seed quality, germination ability and seedling vitality, and finally leads to the large-scale yield reduction of soybean. Seed storage-tolerance is a complex quantitative trait controlled by multiple genes. In order to explore the mechanism of soybean seed storage tolerance, the relevant genes were mined. In this study, 112 recombinant inbred lines derived from the cross of Zhongdou 27 and Jiunong 20 were used as materials to evaluate the storage-tolerance of soybean seeds. Binmap was constructed using 343 907 high-quality SNPs markers, QTLs for storage related traits of soybean seeds were mapped and further analyzed by genome, transcriptome and metabolome. A total of 31 QTLs were obtained in this experiment, distributed on 10 chromosomes of soybean. Through the combined analysis of genome, transcriptome and metabolome, 3 candidate genes related to seed storage tolerance were found, covering 19 metabolic pathways including flavonoid biosynthesis pathways and linoleic acid metabolism etc. The results provided theoretical basis and technical support for further analyzing the genetic architecture of soybean seed storage tolerance and breeding soybean storage tolerance varieties.