(1) Background: Vietnam is a multiethnic country undergoing rapid economic development, the improvement in nutritional status in preschool children is not equally shared by all ethnic groups; (2) Methods: A cross-sectional study was performed from September–December 2018 on 16,177 children aged 24–60 months representing Kinh (n = 14421), Muong (n = 1307) and Tay (n = 449) ethnic groups. Prevalence of malnutrition, overweight, obesity and anthropometric indices were compared across ethnic groups, using WHO 2006 child growth standards; (3) Results: The prevalence of malnutrition among children of Kinh, Muong and Tay origins was 14.7%, 34.3% and 43.2%, respectively. The corresponding data for overweight was 5.5%, 2.7%, 2.2% and for obesity 2.8%, 0.8% and 0.4%, respectively. The prevalence of stunting remained the highest in three subtypes of malnutrition in all ethnic groups. Kinh children were heavier and taller than the other groups, while Muong children were taller than Tay children (p-value < 0.001); and (4) Conclusions: Malnutrition remains a major public health issue among children of minor ethnicities while overweight and obesity is an emerging challenge for the Kinh ethnic group. The results imply that a community-based intervention should be specific to ethnicity to reduce the gap in nutritional status between ethnic groups in Vietnam.