Abstract Background Feeding mode is an important factor affecting the reproductive performance of pigs. The composition and expression of the intestinal microbiota are closely related to the physiological and biochemical indicators of animals. Therefore, to investigate the effects of different feeding modes on the intestinal microbial community structure and reproductive performance of pigs, reproductive performance data were collected from 1607 Yorkshire pigs raised under different feeding modes for fixed-effect variance analysis. Among them, 731 were in the artificial feeding (AM) group, and 876 were in the feeding station feeding (SM) group. Additionally, 40 Yorkshire sows in the late gestation period were randomly selected from each feeding mode for intestinal microbiota analysis. Results The results of the analysis showed that, in the AM group, both the number of born deformity(NBD)and number of stillborn(NSB)were significantly greater than they were in the SM group ( P < 0.05). Additionally, the TNB in the AM group was significantly lower than that in the SM group ( P < 0.05). The results of the intestinal microbiota analysis revealed that at the phylum level, there were significant differences in 9 bacterial taxa between the AM and SM groups ( P < 0.05). At the genus level, the abundance of a variety of beneficial bacteria related to reproductive performance in the SM group was significantly greater than that in the AM group. Differential pathway enrichment analysis revealed that the expression of the Cellular ( P < 0.01) community-prokaryote pathway was significantly lower in the AM group than in the SM group (P < 0.05) . However, the expression of the pathways glycan biosynthesis and metabolism, infectious diseases: viral, cardiovascular diseases, cancers: specific types, neurodegenerative diseases and metabolism of other amino acids was significantly greater in the AM group than in the SM group (P < 0.05). Conclusion These results indicate that different feeding modes can have an impact on the intestinal microbial composition of Yorkshire pigs and further affect the reproductive performance of pigs through the pathway of the intestinal microbiota. The results of this study provide valuable insights for further exploring the relationships between feeding modes, intestinal microbial composition, and host phenotypes.