At present, there is insufficient evidence on whether prenatal multi-micronutrient (MM) supplementation can be an antenatal nutritional intervention or not. This study aimed to explore the sustained effect of prenatal MM supplementation on early childhood health. A total of 939 mother−offspring pairs were followed up in the study between 2015 to 2018 in Changsha, China. Information was mainly collected through household surveys at the ages of 1, 3, 6, 8, 12, 18, 24, and 36 months. General linear models and generalized estimating equation models were used to estimate the effects of maternal prenatal MM compared with IFA supplementation on infant growth and development. Offspring of women who used prenatal MM compared with IFA supplements had lower weight-for-age z score (WAZ) (adjusted β: −0.23, 95% CI: (−0.40, −0.06)) and weight-for-length z score (WLZ) (adjusted β: −0.20, 95% CI: (−0.37, −0.02)) at 3 months old, but a reduced risk of obesity at birth (aRR: 0.30, 95% CI: 0.11−0.78) and being overweight at 3 months old (aRR: 0.52, 95% CI: 0.32−0.84). Moreover, offspring of women who used prenatal MM compared with IFA supplements had significantly higher scores for communication (adjusted β: 0.41, 95% CI: 0.61−0.21), gross motor (adjusted β: 0.68, 95% CI: 0.49−0.88), fine motor (adjusted β: 1.64, 95% CI: 1.45−1.84), problem solving (adjusted β: 0.29, 95% CI: 0.10−0.49), and personal−social (adjusted β: 0.90, 95% CI: 0.70−1.10) skills at 36 months old. Prenatal MM supplementation could result in better infant growth in the first few months of life and improve development scores at the age of 3 years compared with IFA supplementation.