Background Adequate nutrition is needed to ensure optimum growth and development of infants and young children. Although the national economy has developed rapidly during recent decades in China, malnutrition continues to be a major public health problem. The aim of the present study was undertaken to assess the prevalence and risk factors associated with stunting and severe stunting under 3 years old in mid‐western rural areas in China. Methods A community‐based cross‐sectional survey was carried out in 84 villages in mid‐western provinces of China in 2010. A total of 1260 children were selected for nutritional assessment in terms of stunting and severe stunting using the new World Health Organization growth standards. Hierarchical logistic regression was used to examine the risk factors for adverse nutritional status. Results The prevalence of stunting and severe stunting was 27.0% and 13.2% respectively. Hierarchical logistic regression analysis showed that the risk factors for stunted children were province of residence, caregiver's education, child's gender, low birthweight and duration of exclusive breastfeeding (<6 months). The risk factors for severe stunting in children aged 0–36 months were province of residence, caregiver's education and child's gender. Conclusions These results indicate that malnutrition is still a major public health problem among children under 3 years old. The government should implement appropriate nutritional intervention strategies to help reduce the prevalence of malnutrition in children.