Obesity is a complex system problem involving a broad spectrum of policy, social, economic, cultural, environmental, behavioural, and biological factors and the complex interrelated, cross-sector, non-linear, dynamic relationships among them. Systems modelling is an innovative approach with the potential for advancing obesity research. This study examined the applications of systems modelling in obesity research published between 2000 and 2017, examined how the systems models were developed and used in obesity studies and discussed related gaps in current research. We focused on the applications of two main systems modelling approaches: system dynamics modelling and agent-based modelling. The past two decades have seen a growing body of systems modelling in obesity research. The research topics ranged from micro-level to macro-level energy-balance-related behaviours and policies (19 studies), population dynamics (five studies), policy effect simulations (eight studies), environmental (10 studies) and social influences (15 studies) and their effects on obesity rates. Overall, systems analysis in public health research is still in its early stages, with limitations linked to model validity, mixed findings and its actual use in guiding interventions. Challenges in theory and modelling practices need to be addressed to realize the full potential of systems modelling in future obesity research and interventions.