With over 1·3 million Anganwadi centres (AWC) (meaning ‘courtyard shelter’), the Indian government runs a nationwide intervention providing nutrition supplement to pregnant mothers to improve the health of their children. Using two successive rounds of the nationally representative cross-sectional National Family Health Survey data (collected during 2005–2006 and 2015–2016) of India, we assessed whether nutrition supplements given to pregnant mothers through AWC were associated with select child health indicators – extremely low birth weight (ELBW), very low birth weight (VLBW), low birth weight (LBW) and neonatal mortality (death during day 0–27) stratified by death during day 0–1, day 2–6 and day 7–27. A total of 148 019 children and 205 593 children were eligible for analysing birth weight and neonatal mortality, respectively. OR with 95% CI, estimated from multivariate logistic regression models, suggest that receipt of nutrition supplements was associated with decreased risk of VLBW (OR: 0·73, 95% CI 0·63, 0·83, P < 0·001), LBW (OR: 0·92, 95% CI 0·88, 0·96, P < 0·001), but not ELBW (OR: 0·80, 95% CI 0·56, 1·15, P = 0·226). Women who always received nutrition supplements during their pregnancy saw lower risk of death of their neonates (OR: 0·67, 95% CI 0·61, 0·73, P < 0·001), including death on day 0–1 (OR: 0·66, 95% CI 0·58, 0·74, P < 0·001), day 2–6 (OR: 0·69, 95% CI 0·58, 0·82, P < 0·001) and day 7–27 (OR: 0·68, 95% CI 0·53, 0·87, P = 0·002). Therefore, nutritional supplementation to pregnant mothers appears to be helpful in deterring various stages of neonatal mortality, VLBW and LBW, though it might not be effective in mitigating ELBW. Findings were discussed considering possible limitations of the study.