India has one of the highest burdens of childhood undernutrition in the world. The two principal dimensions of childhood undernutrition, namely stunting and underweight can be significantly associated in a particular population, a fact that is rarely explored in the extant literature. In this study, we apply a copula geoadditive modelling framework on nationally representative data of 104,021 children obtained from the National Family Health Survey 5 to assess the spatial distribution and critical drivers of the dual burden of childhood stunting and underweight in India while accounting for this correlation. Prevalence of stunting, underweight and their co-occurrence among under 5 children were 35.37%, 28.63% and 19.45% respectively with significant positive association between the two (Pearsonian Chi square = 19346, P-value = 0). Some of the factors which were significantly associated with stunting and underweight were child gender (Adjusted Odds Ratio (AOR) = 1.13 (1.12) for stunting (underweight)), birthweight (AOR = 1.46 (1.64) for stunting (underweight)), type of delivery (AOR = 1.12 (1.19) for stunting (underweight)), prenatal checkup (AOR = 0.94 (0.96) for stunting (underweight)) and maternal short-stature (AOR = 2.19 (1.85) for stunting (underweight)). There was significant spatial heterogeneity in the dual burden of stunting and underweight with highest prevalence being observed in eastern and western states while northern and southern states having relatively lower prevalence. Overall, the results are indicative of the inadequacy of a “one-size-fits-all” strategy and underscore the necessity of an interventional framework that addresses the nutritional deficiency of the most susceptible regions and population subgroups of the country.