Currently, the importance of gut microbiota to the health of their host has been well discussed, yet the knowledge about the host hormonal effect on the gut microbiota is limited. In this study, a combination of the high-throughput 16S rRNA gene-based pyrosequencing and the Mass Spectrometry (MS)-based metabolomics techniques were used to investigate the stool microbial composition and microbial metabolites at different gestation day in Meishan sows. The results showed that, the stool steroid hormones including estradiol (E 2 ), progesterone (P 4 ) and cortisol (CORT) were increased at gestation day 90 (P<0.05), when compared to gestation day 30. In coincide with the changes of steroid hormones, the relative abundance of Burkholderiales and Selenomonadales of the stool microbiota at d90 of pregnancy was significantly increased than that of at d30 of pregnancy at the order level (P<0.05). However, no significant difference of the richness estimators (ACE and Chao), and the diversity indices (Shannon and Simpson) were found between the d30 and d90 of gestation. Further, the metabolomics profile revealed 13 metabolites changed greatly from the gestation day 30 to 90, including amino acid metabolic pathway, lipid and carbohydrate metabolic pathway (P<0.001). The results suggest that the interaction of the steroid hormones and the gut bacteria may account for the metabolic changes throughout the length of pregnancy.