India has witnessed increasing trends in internal migration over the last three decades. In India, migrant children are not a homogeneous group and their reasons for movement and vulnerabilities vary across socio-economic stratum. For some children, migration may open possibilities and is associated with expanding social and economic spheres, but for many others, it may bring serious risks. Therefore, the study has been carried out to understand socio-economic vulnerability in child nutrition with migration status and other contributing factors in India. This study used data from the National Family Health Survey, the fourth in the NFHS series which was conducted in 2015–2016 (NFHS-4). We were interested in looking at the children age 12–59 months for their nutritional indicators such as stunting and underweight across migrants and non-migrants children. This resulted in a sample of 199,448 children in selected age group and among them 33.1% children belongs to the migrant family as compared to 67% of non-migrant children. Overall, 44.2% of children were stunted and 39.5% were underweight among non-migrant children as compared to 37.4% & 32.8% of migrant children were stunted and underweight respectively. Further, the results showed that among the social groups, scheduled caste children were found a high variation in underweight (34% vs. 41.6%) and stunting (36% vs. 46%) between migrants and non-migrants children. Similar trend of malnourishment is found in the poor wealth quintile, for rural residents and low educated women with non-migrant status. Those children who were poor but non-migrant were more likely to be malnourished as underweight [aOR; 1.15, CI: 1.11–1.18] and stunted [aOR; 1.17, CI:1.13–1.20] as compared to migrant status children in the same category of the household. Similarly in reference to scheduled caste migrant group, the scheduled caste non-migrant were more likely to be underweight [aOR; 1.15, CI: 1.09–1.20] and stunted [aOR; 1.18, CI: 1.12–1.23] than the children with migrant status. There were huge differences between migrant and non-migrant children in nutritional statuses. Education, caste and wealth index are found to be an important variables to explain the differential between migrants and non-migrants in child’s nutritional aspects. Children associated with poor socio-economic vulnerability and non-migrant category need to be taken care of more and a community targeted approach is required to understand the gaps. The programs such as ICDS, and Poshan Abhiyan need to be revamped adding the migration aspect of the families and children in terms of their health and nutritional aspects.