The resilience of cities in response to natural disasters and long-term climate change has emerged as a focus of academic and policy attention. In particular, how to understand the interconnectedness of urban and natural systems is a key issue. This paper introduces an urban model that can be used to evaluate city resilience outcomes under different policy scenarios. The model is the Wellington Integrated Land Use-Transport-Environment Model (WILUTE). It considers the city (i.e., Wellington) as a complex system characterized by interactions between a variety of internal urban processes (social, economic and physical) and the natural environment. It is focused on exploring the dynamic relations between human activities (the geographic distribution of housing and employment, infrastructure layout, traffic flows and energy consumption), environmental effects (carbon emissions, influences on local natural and ecological systems) and potential natural disasters (e.g., inundation due to sea level rise and storm events) faced under different policy scenarios. The model gives insights that are potentially useful for policy to enhance the city’s resilience, by modelling outcomes, such as the potential for reduction in transportation energy use, and changes in the vulnerability of the city’s housing stock and transport system to sea level rise.