This study aimed to identify critical risk factors for childhood malnutrition and inform targeted interventions. Childhood malnutrition remains a pressing concern in the coastal regions of Bangladesh. Data were extracted from the latest Bangladesh Demographic and Health Survey 2017–2018 and children aged 0–59 months and their mothers aged 15–49 years from 17 coastal districts were included as study population in this study. We performed multivariable logistic regression model to determine the risk factors and a total 2153 children were eligible for the analysis. Stunting, wasting and underweight prevalence was 31.4%, 8.5% and 21.1% respectively. Stunting was more common in children aged 24–35 months with compared to their younger counterparts [adjusted odds ratio (AOR) = 3.32, 95% confidence interval (CI): 2.35–4.67]. Children to mothers with higher education exhibited 69% (AOR = 0.31, 95% CI: 0.18–0.52) lower risk of stunting compared to those with no education. Similarly, children in poorest and poorer households had 2.2 and 1.83 times higher odds of stunting respectively than those in the richest households. Children born to obese mothers (compared to normal) were 34% less likely to be stunted (AOR = 0.66, 95% CI: 0.51–0.85). Children who had fever and underweight mothers reported wasting. Increasing child age, low maternal education, poorest wealth index, unimproved toilet facilities and childhood morbidity were identified as significant risk factors for underweight. Results support the requirement of effective and appropriate interventions for this particular region considering the identified risk factors to reduce childhood malnutrition in Bangladesh.