Ecological risk regionalisation is a process for determining the distribution of eco-risk. The basis of ecological risk regionalisation is regional ecological risk assessment. Existing procedures for ecological risk assessment often aim at natural ecosystems and are used mainly for retrospective evaluation of risks. This paper presents a tiered ecological risk assessment procedure (TERAP) for complex ecosystems. The approach is not only for current evaluation, but also for retrospective and future evaluations. Based on the TERAP, a regional ecological risk assessment model was constructed. The TERAP has three tiers: the first is demarcation of the area affected by a particular stressor; the second is a semi-quantitative assessment of the risk index A07112; which is gained from the vulnerability index and integrated into the hazard index; the third is quantitative loss evaluation under the risk index. The main factors in the ecological risk assessment model are ecosystem attributes and socio-economy status. According to the main factors in the model, the change in the ecosystem into the future is simulated and the socioeconomic mathematical model is constructed. In this paper, taking Chongming Island as an example, the approach taken for simulation of the future ecosystem is analysis with the CLUE-S model. The end purpose of current and future ecological risk regionalisation is to direct region programming and risk management.