(1) Background: Maternal diet and alcohol consumption can influence both maternal and infant's gut microbiota. These relationships are still not examined in the Chinese population. The purpose of this study was to explore the effect of alcohol consumption and maternal diet during pregnancy on maternal and infant's gut microbiota. (2) Methods: Twenty-nine mother-child dyads were enrolled in central China. Fecal samples of mothers during late pregnancy and of newborns within 48 h were collected. The V3-V4 regions of 16S rRNA sequences were analyzed. A self-administrated questionnaire about simple diet frequency in the past week was completed by mothers before childbirth. The demographic information was finished by mothers at 24 h after childbirth. (3) Results: Among these 29 mothers, 10 mothers reported alcohol consumption during pregnancy. The PCoA (β-diversity) showed significant difference in maternal gut microbiota between the alcohol consumption group vs. the non-alcohol consumption group (abund-Jaccard, r = 0.2, p = 0.006). The same phenomenon was observed in newborns (unweighted-UniFrac full tree, r = 0.174, p = 0.031). Maternal alcohol consumption frequency showed positive associations with maternal Phascolarctobacterium (p = 0.032) and Blautia (p = 0.019); maternal Faecalibacterium (p = 0.013) was negatively correlated with frequency of alcohol consumption. As for newborns, a positive relationship showed between Megamonas (p = 0.035) and newborns with maternal alcohol consumption. The diet was not associated with both maternal and infant's gut microbiota. (4) Conclusions: Maternal alcohol consumption during pregnancy influenced the gut microbiota on both mothers and the newborns. Future research is needed to explore these relationships in a lager birth cohort. Understanding the long-term effect of alcohol consumption on maternal and newborns' gut microbiota is needed.