<p>Child malnutrition poses a serious threat to low-income households in developing countries. It has long-term effects on economic growth. The crop diversity has recently been taken into consideration as a means of enhancing health and nutrition. However, a dearth of research highlights the actual connection between the impacts of crop diversification and the nutritional standing in the eastern part of India. To fill this knowledge gap, the present study is a novel attempt to investigate how crop diversification affects childhood malnutrition, determine the factors associated with malnutrition, and execute proper policies and actionable insights to minimize the status of child malnutrition in the eastern part of India. The NFHS-5 round (2019–21) data and the web-based Land Use Statistics data for the 2020–21 agricultural year were used. Results indicate that districts located in eastern India with a high crop diversification index, particularly in the eastern regions, exhibit lower rates of childhood malnutrition, including stunting, wasting, and underweight. Conversely, districts with lower crop diversification, primarily located in the central and western regions, show higher prevalence rates of these malnutrition indicators. The study found that increasing the crop diversification index is significantly associated with decreasing child wasting and the burden of being underweight. However, it is not significantly associated with stunting. The multivariate analysis also highlights the significant impact of other covariates on child nutrition. This study will be applicable and helpful to planners, policymakers, and researchers for executing proper policies to reduce inter-district disparities in child malnutrition in various regions of India and other developing nations.</p>