Being born with appropriate weight-for-gestational age (AGA, ~80% of newborns) is often considered as low risk for future obesity. This study examined differential growth trajectories in the first two years by considering pre- and peri-natal factors among term-born AGA infants. We prospectively investigated 647 AGA infants and their mothers enrolled during 2012–2013 in Shanghai, China, and obtained repeated anthropometric measures at ages 42 days, 3, 6, 9, and 18 months from postnatal care records, and onsite measurements at age 1 and 2 years (skinfold thickness, mid-upper arm circumference (MUAC)). Birthweight was classified into sex-and gestational age-specific tertiles. Among mothers, 16.3% were overweight/obese (OWO), and 46.2% had excessive gestational weight gain (GWG). The combination of maternal prepregnancy OWO and high birthweight tertile identified a subset of AGA infants with 4.1 mm higher skinfold thickness (95% CI 2.2–5.9), 1.3 cm higher MUAC (0.8–1.7), and 0.89 units higher weight-for-length z-score (0.54, 1.24) at 2 years of age with adjustment for covariates. Excessive GWG was associated with higher child adiposity measures at 2 years of age. AGA infants manifested differential growth trajectories by the combination of maternal OWO and higher birthweight, suggesting that additional attention is needed for those “at increased risk” of OWO in early intervention.