Several studies have shown that an increased risk of metabolic and immune disorders associated with cesarean section mode of delivery may exist. However, such studies have not been conducted in the Chinese population. Stool sample sequencing of the gene encoding the 16S rRNA of 82 prospectively enrolled 3- and 30-42-day-old vaginal and cesarean section delivered newborns was performed to study the composition and predicted function of the intestinal microbiota. In the samples from the 3-day-old neonates, the levels of in the two groups were similar. The genera , and were more prominent in the vaginal delivery than in the cesarean section group, which showed a predominance of , and . The differences between the two groups were statistically significant ( < 0.05). In the samples from 30- to 42-day-old infants, , and were the main genera present in the vaginal delivery group, while in the cesarean section delivery group; the predominant genera were , and . Predicted functions of the vaginal delivery group revealed higher metabolic and biodegradation rates of carbohydrates, vitamins, and xenobiotics than those in the cesarean section group, which contributed to the stability of the microbiota in the former. The abundance of probiotic bacteria such as and , and the negative correlation between obesity and presence were higher in vaginally delivered infants than in cesarean-delivered infants at both studied time points.