The vitamins in infants who are exclusively breastfed before 6 months of age mainly come from breastfeeding. Whether or not dynamic vitamin concentrations in human milk were affected by maternal factors and their roles in infant growth and diseases has yet to be determined. Using data from a tertiary hospital for 46 couples of fit mothers and infants aged 1 to 3 months in China, we collected mothers' human milk as samples for UPLC-MS/MS sequencing evaluation of vitamins. Multiple regression and binomial logistic regression were used in analyses that controlled for confounding. The content of vitamin B1 was significantly higher at 105 to 119 days postpartum than it was at 30 to 44 days after delivery (p < 0.05). Additionally, vitamin C was related to infant weight-for-age (beta = 0.05, SE = 0.02, p = 0.02). Vitamins C (beta = 0.00015, SE = 0.00006, p = 0.01) and B7 (beta = 0.00048, SE = 0.00023, p = 0.04) were related to infant BMI. After adjustment for sample collection times, vitamins A and B1, the odds ratio for vitamin K in the BMJ group was 13.93 (95% CI, 0.93 to 208.48, p = 0.05). Overall, the vitamin B1 contents from human milk change in different stages of lactation. A longer duration of fully breastfeeding with vitamins B7 and C provides better developmental nutrients to infants aged 1 to 3 months. According to our study, vitamin K concentration seems to be increased in the human milk of mothers whose infants had BMJ.