Background: Whole-of-community interventions have been recommended and show promise for preventing obesity; however, research to understand the mechanisms underlying their success or failure is lacking. Complex systems approaches may be useful to address this gap. Purpose: To describe the evolution and utilization of qualitative and quantitative complex systems methods to understand and model whole-of-community obesity prevention interventions. Approach: We illustrate the retrospective qualitative development of a systems map representing community change dynamic within the Shape Up Somerville (SUS) intervention. We then describe how this systems map, and complementary work of other successful obesity prevention interventions (Romp & Chomp intervention), informed the COMPACT (childhood obesity modeling for prevention and community transformation) study. COMPACT's design aligns complex systems science principles and community-engaged research to better understand stakeholders' leadership roles in whole-of-community interventions. We provide an overview of the complex systems tools used in COMPACT: agent-based modeling, group model building, and social network analysis and describe how whole-of-community intervention stakeholders ("agents") use their social networks to diffuse knowledge about and engagement with childhood obesity prevention efforts, laying the groundwork for community readiness for sustainable change. Conclusion: Complex systems approaches appear feasible and useful to study whole-of-community obesity prevention interventions and provide novel insights that expand on those gained from traditional approaches. Use of multiple methods, both qualitative and quantitative, from the complex systems toolkit working together can be important to success. [This article was written on behalf of the SUS Systems Map Team and the COMPACT Team.]