In the process of rapid urbanisation in China, environmental problems have increased, from sewage discharge to climate change. Marine protected areas (MPAs) are widely advocated as a means to comprehensively manage human activities and resources in ocean and coastal areas. However, MPAs only safeguard populations or assemblages within their boundaries and fail to offer any protection from many major threats to marine environments. An increase in environmental threats implies an increase in environmental management and assessment. We propose a methodological framework for integrated ecological assessment using the Xiamen marine protected area as a case study. The integrated ecological assessment framework can be generalised from the dimensions of environment, economy, society and institution. Surveys were undertaken to assess the state of the Xiamen coastal environment, the resources of the reserve, and issues associated with human activities. Stakeholders were interviewed about their attitudes towards issues regarding the management of the reserve. The constraints of the reserve management were identified. The methodological framework is presented as a tool to help identify relative ecological security in order to prioritise actions and assess the ecological implications of management and policy decisions.