Abstract Background Nutritional inequality in India has been estimated typically using stunting, wasting and underweight separately which hide the overall magnitude and severity of undernutrition. We used the Composite Index of Anthropometric Failure (CIAF) that combines all three forms of anthropometric failures to assess the severity of undernutrition and identify the most vulnerable social groups and geographical hotspots. Method CIAF was constructed using child anthropometric data from the fourth round of the National Family Health Survey (NFHS-4, 2015–16). We considered 24 intersecting sub-groups based on intersections across four main axes of inequality i.e., caste [Scheduled Tribe (ST), Scheduled Caste (SC) and Other], economic position (poor and non-poor), place of residence (rural and urban) and gender (male and female) (eg. ST-Poor-Rural-Female). Cross-tabulation and logistic regression were done to assess the odds of CIAF among intersecting groups and to identify the most vulnerable sub-groups. Concentration curve was plotted to visualise economic position inequality in child undernutrition across caste categories. Choropleth maps were constructed and descriptive analysis of the district-level prevalence of CIAF was performed to identify the geographic clustering of undernutrition. Results Overall 55.32% of children were undernourished by CIAF and 6.62% of children have simultaneous three anthropometric failure. In sub-group analysis, children from ST and SC caste have a higher risk of undernutrition irrespective of other axis of inequality. Compared with CIAF, economic position inequality was amplified for simultaneous-three-failures among all caste categories. Economic position inequalities within caste are more for other caste and SC categories than with ST. Economic position, caste and gender based inequality in all three failures is more consistent in rural areas than with urban areas. Based on the analysis of the high prevalence in the co-occurrence of two or three failures, 111 districts from 12 of 29 states in India were identified across four geographic clusters. Conclusions The study shows social and eco-geographical clustering of multi-dimensional anthropometric failures and indicates the need for focused nutritional interventions among SC and ST community in general and ST children from the poor households. Furthermore, governance interventions that target entire regions across districts and states combined with decentralised planning are needed.