In order to protect the biodiversity and the depleted marine resources, we should reserve them for future generations.Therefore, try to introduce the concept of Marine Protected Areas ( MPAs) which are based on ecosystem. It is divided into different kinds of protected areas to reserve the resources and protect the biodiversity and the completeness of natural habitats. MPAs offer the foundation of natural Sustainable Development. According to this research, and use the theory of resource economics basis to discuss the effective of MPAs. Then, it continued to discuss the effective of MPAs which is under negative uncertainty. According to the evidence of results, MPAs indeed can reap the benefit of our ecological at the same time , it also can maintain the effectiveness of MPAs.