Abstract: In order to explore the biosynthesis mechanism of the sanxiapeptin, the BGISEQ-500 platform was used to determine cDNA library when the SG-4 was cultured at 200 mL for 4, 7 d and 300 mL for 7 d, and RNA-seq analysis 6.42 Gb data generated by high-throughput sequencing without reference genome. The results showed that the transcriptome sequence alignment rate was as high as 93.88%, it was found that the differential genes were mainly concentrated in the pathways of antibiotic synthesis, substance transport and redox metabolism. In the non-ribosomal peptide synthetase (NRPS, Non-ribosomal peptide synthetase) gene cluster PDE_01071, the expression trends of 21 genes were completely consistent with the content of substances, it suggested that the gene cluster PDE_01071 might be responsible for the synthesis of sanxiapeptin.