Coral reefs are among the most fragile ecosystems that provide essential services to local Small Island Developing States (SIDS) communities. As such, exploring the characteristics and interactions shaping regime shifts of coral reefs is of paramount importance in managing system pressures; enhancing resilience; aiding their regeneration and recovery process; and restoring habitat complexity. However, understanding the dynamics of coral reef ecosystems regime shift requires employing an approach capable of dealing with systems being affected by multiple climatic and socio-economic non-climatic pressures as well as an effective treatment of systemic embedded uncertainties. This study applies Fuzzy Cognitive Mapping (FCM) in a participatory stepwise and systematic procedure to reflect dynamic casualties and temporal changes of coral reef ecosystem regime change over a long-time perspective. This mapping technique allows conceptualising dynamic models to represent causalities and modelling input values to simulate fluctuations within a complex temporal system. Port Resolution on Tanna Island in Vanuatu was selected as the case study region representative of Pacific-SIDS geography and human communities. As an initial outcome and an indicator of multidisciplinary of this study, twenty-seven principal influential factors and their corresponding causal relationships were identified. Subsequently, the coral reef regime shift was analysed under four main plausible scenarios representing major climatic and non-climatic trajectories. The results indicate that climate change factors play pivotal roles in the regime shift of the coral reef ecosystem globally. At the focal scale of this study, the tourism industry and coral fisheries are the most vulnerable services provided by coral reefs. As such, coupled local management interventions and global efforts in mitigating the adverse impacts of climate change is likely to yield better coral reef ecosystem services at a local community level.