In China, with fast economic growth, health and nutrition status among the rural population has shown significant improvement in the past decades. On the other hand, burden of non-communicable diseases and prevalence of related risk factors such as overweight and obesity has also increased. Among rural children, the double burden of malnutrition and emerging overweight and obesity has been neglected so far. According to the theory of Developmental Origin of Health and Diseases (DOHaD), malnutrition, including both undernutrition (stunting and wasting) and over-nutrition (overweight and obesity) during childhood is closely related to worsened health outcomes during adulthood. Such a neglected problem is attributable to a complicated synergy of social and environmental factors such as parental migration, financial situation of the household, child-rearing knowledge and practices of the primary caregivers, and has implications for public health. Based on literature review of lessons from the field, intervention to address malnutrition among rural children should be a comprehensive package, with consideration of their developmental environment and geographical and socioeconomic diversity. The scientific evidence on DOHaD indicates the probability and necessity of prevention of adult disease by promotion of maternal and child health and reducing malnutrition by provision of high-quality complementary foods, promotion of a well-balanced dietary pattern, and promotion of health literacy in the public would bring a potential benefit to reduce potential risk of diseases.