Background: We aimed to examine whether the Healthy Children, Healthy Families, and Healthy Communities Program, consisting of multi-level strategies for obesity prevention tailoring the context of socioeconomically vulnerable children based on an ecological perspective, would be effective on improving their healthy lifestyle behaviors and obesity status. Methods: Participants were 104 children (and 59 parents) enrolled in public welfare systems in Seoul, South Korea. Based on a cluster-randomized controlled trial (no. ISRCTN11347525), eight centers were randomly assigned to intervention (four centers, 49 children, 27 parents) versus control groups (four centers, 55 children, 32 parents). Multi-level interventions of child-, parent-, and center-level strategies were conducted for 12 weeks. Children’s healthy lifestyle behaviors and obesity status were assessed as daily recommended levels and body mass index ≥85th percentile, respectively. Parents’ parenting behaviors were measured by the Family Nutrition and Physical Activity scale. Results: Compared to the control group, the intervention group showed significant improvements in total composite scores of healthy-lifestyle behaviors—including 60-min of moderate physical activity—but not in obesity status among children. Moreover, the intervention group showed significant improvements in parenting behaviors among parents. Conclusion: The multi-level strategies for obesity prevention based on an ecological perspective may be effective for promoting healthy lifestyles among socioeconomically vulnerable children.