The purpose of this study was to compare the effects of different infant formulas on the growth and development, sleep, allergy symptoms, and intestinal flora of infants. A total of 428 infants participated in the study. Breastfeeding (BF) was used as the control, and the remaining subjects were randomly assigned to the full goat milk protein formula group (FGM), partial goat milk protein formula group (PGM), and cow milk formula group (M). During the 6-month feeding experiment, data on the growth, sleep, allergy symptoms, and intestinal flora of infants were collected using questionnaires, anthropometric measurements, and biochemical examinations. In general, the basic information of the participants was consistent among the groups. There were no differences in infant weight, length, or head circumference among the groups (p > .05). The sleep time of infants in the formula-fed groups was longer than that of the breastfeeding group at baseline (p < .05), but there were no differences at mid-term or outcome (p > .05). The incidence of allergic symptoms continued to decrease, and the total scores of allergic symptoms did not differ among the groups (p > .05). The relative abundance of intestinal Bifidobacteriaceae in the PGM group was lower than that in the other groups (p < .05). There was no difference in the β-diversity of intestinal flora between formula-fed and breastfed infants (p > .05). There were strong correlations in the composition of the main intestinal flora at the family level between the formula and breastfeeding groups. This study showed that within 6months of feeding, there were no significant differences in the growth and development, allergic symptoms, or intestinal flora of the infants among the groups.