This study examines malnutrition’s triple burden, including anaemia, overweight, and stunting, among children aged 6–59 months. Using data from the National Family Health Survey-5 (2019–2021), the study identifies risk factors and assesses their contribution at different levels to existing malnutrition burden. A random intercept multilevel logistic regression model and spatial analysis are employed to identify child, maternal, and household level risk factors for stunting, overweight, and anaemia. The study finds that 34% of children were stunted, 4% were overweight, and 66% were anaemic. Stunting and anaemia prevalence were higher in central and eastern regions, while overweight was more prevalent in the north-eastern and northern regions. At the macro-level, the coexistence of stunting, overweight, and anaemia circumstantiates the triple burden of childhood malnutrition with substantial spatial variation (Moran’s I: stunting-0.53, overweight-0.41, and anaemia-0.53). Multilevel analysis reveals that child, maternal, and household variables play a substantial role in determining malnutrition burden in India. The nutritional health is significantly influenced by a wide range of determinants, necessitating multilevel treatments targeting households to address this diverse group of coexisting factors. Given the intra-country spatial heterogeneity, the treatment also needs to be tailor-made for various disaggregated levels.