Using bioinformatics technology, the molecular biological mechanism of Brassica rapa regulating intestinal immune function was explored. Methods Male BALB/ C mice were randomly divided into three groups, with 6 mice in each group. SC1 group was gavaged with Brassica rapa extract, SC2 group was gavaged with chopped Brassica rapa slurry suspension, and NC group was gavaged with normal saline once a day for 7 consecutive days as blank control. RNA was extracted from small intestine tissue samples of each group, and transcriptome sequencing was performed after the total RNA was qualified. Cluster analysis of differentially expressed genes was performed according to GO function and KEGG signaling pathway, and mapping revealed immune-related pathways with highly enriched differentially expressed genes. The changes of gene expression in small intestine of Brassica rapa sinensis mice were analyzed from immune Angle. Results The expression of 27733 mRNA was detected by transcriptome sequencing. Compared with NC group, there were 1635 differentially expressed genes in SC1 group, including 1236 differentially expressed genes up-regulated and 399 differentially expressed genes down-regulated. Compared with NC group, 2872 genes were significantly differentially expressed in SC2 group, including 2233 up-regulated genes and 639 down-regulated genes. Cluster analysis of GO function and KEGG signaling pathway showed that the enrichment degree of differentially expressed genes in interleukin secretion, interferon response, T cell receptor signaling pathway and vitamin and fat digestion and absorption were among the top 20 in both Brassica rapa groups. Immunoprotein-coding genes such as intestinal mucosa chemokine CCL20 and macrophage polarization marker CD274 were significantly differentially expressed and belonged to the above immune pathways(P＜0.05). Conclusion The differentially expressed genes in the small intestine were highly enriched in interleukin secretion, interferon response, T cell receptor signaling pathway and nutrient digestion and absorption, suggesting that The function of intestinal immune system and intestinal mucosa was regulated by Brassica rapa. The up-regulated expression of Cd274 and down-regulated expression of Ccl20 suggest that the induction of polarization of M1-type macrophages and activation of T cells may be an important way to regulate the immunity and maintain the normal intestinal structure and function.