Malnutrition occurs when a person’s diet does not provide adequate nutrients for growth and health or when the body cannot absorb nutrients properly. It is one of the biggest burdens of recent years covering both overnutrition and undernutrition. Undernutrition is usually marked based on height, weight, and age and measured with stunting, wasting, and underweight. According to the World Health Organization (WHO), around 1.9 billion adults are overweight, while 462 million are underweight worldwide. Therefore, it is necessary to target undernutrition, especially among Under-5 (U-5) children. The data under study was taken from the fifth round (2019–21) of National Family Health Survey (NFHS-5). This study highlights the issue of malnutrition and its associated factors among U-5 children measured in terms of stunting, wasting, and underweight. The analysis considers factors at three levels: mother, child, and household. Logistic regression was used to identify the variables that are statistically significant in relation to stunting, wasting, and underweight. Results revealed that about 35.4% of children were stunted, 18.6% wasted and 31.0% underweight. As compared to a male child, the female child suffered more. The key factors linked to malnutrition among children under five in India were the mother’s age, education, cesarean delivery, child’s birth size, wealth status, and place of residence. Nutritional education is crucial for raising awareness among people about the importance of balanced and nutritious food choices. Effective implementation of targeted nutrition programs, addressing the specific needs and priorities of pregnant mothers and undernourished children, can play a significant role ineradicating stunting, wasting, and underweight issue in children.