This study investigates the spatial predictors of malnutrition among children aged 0–2 years in India. Using data from the National Family Health Survey-4 (NFHS-4), a structural equation model was developed to determine the direct, indirect, and total effects of various determinants on stunting, wasting, and underweight. Spatial analysis was employed to identify geographical hotspots of key factors influencing malnutrition. Results showed a strong direct relationship between diarrhea, exclusive breastfeeding, and the prevalence of stunting, wasting, and underweight. Indirect effects were observed for maternal education, residence, and desired pregnancy. Spatial analysis revealed significant clustering of factors such as diarrhea, poor drinking water sources, and poor sanitation. The study concludes that interventions focused on the first 1000 days of life, addressing diarrhea, promoting exclusive breastfeeding, and improving sanitation and access to healthcare, are crucial for reducing child malnutrition in India.