Abstract: Somatic embryogenesis is one of the most important ways in soybean regeneration system. In order to explore the differentialy expressed genes in different parts of different developmental stages of soybean induced by somatic embryos, and then analyze the biological processes related to the induction rate, we used the explants of the immature embryo cotyledon of soybean cultivar Heinong 84 to induce somatic embryogenesis at three different stages（0, 15 and 30 d）, the transcriptome of immature cotyledons was sequenced on the adaxial, abaxial surfaces and somatic embryos. The differentialy expressed genes（DEGs） related to somatic embryogenesis in soybean were obtained by sequencing. We screened and enriched different genes at various stages according to GO and KEGG,excavated important genes related to somatic embryo induction, analyzed the primary biological metabolic pathways of each stage and plot their action network, and then analysis the major metabolic pathways during cell embryo-induced development. The results showed that the three stages of DEGs were mainly in the biological processes of hormone induction, photosynthesis, redox, transcriptional regulation and signal transduction. The enrichment analysis of anabolic pathway showed that DEGs mainly concentrated in metabolic pathway, biosynthesis of secondary metabolites, plant hormone signal transduction, ribosome, photosynthesis pathway and so on. The metabolic pathway interaction suggests that the basal metabolic pathway is at the core of somatic embryogenesis.