Abstract: The transcriptome sequencing technology was used to analyze the difference of gene expression in different developmental stages of Ziziphi spinosae semen, and the related genes of the biosynthesis pathway of flavonoids in Ziziphi spinosae semen were identified, which laid a foundation for further analysis of the enzymes related to biosynthesis of flavonoids. Three samples of Ziziphi spinosae semen at different growth and development stages were used as test materials. Illumina Hiseq 4000 was used for transcriptome sequencing, and the transcripts were functionally annotated and differentially analyzed. A total of 74 472 transcripts were obtained by StringTie software assembly, of which 26.83% were annotated in NR, Swiss-Prot, Pfam, GO, KOG, KEGG databases. Metabolic pathway analysis found that flavonoids in the transcriptome of Ziziphi spinosae semen the 11 differen tially expressed genes associated with the synthetic pathway may encode some of the enzymes of the spinosin synthesis pathway. The transcript information of flavonoids in Ziziphi spinosae semen provided an important basis for clarifying the accumulation of spinosin in the growth phase, and a reference for improving the quality of it.