The intensive sea use refers to a centralized development mode with multiple marine reclamation projects in a specific area which were uniformly planned and deployed. Compared with traditional extensive marine reclamation, the intensive sea use is relatively more efficient, ecological and scientific, and is also an effective action to promote the coordinative development of society, economy and marine environment. However, the intensive sea use would also inevitably disturb the marine ecosystem, even result in marine environmental pollution and ecological destruction. Therefore, it is very important to minimize and evaluate the impact of the intensive sea use projects on marine ecosystem. In the present study, main content, thought and process of marine ecological impact assessment were stated by analyzing the impacts of the intensive sea use projects on marine ecosystem, and the evaluation index system is constructed based on habitat quality and ecological response from biotic and abiotic factors in marine ecosystem. Habitat quality, including water environment, sedimentary environment and biological quality index of typical species, reflects the changes of marine habitats affected by the intensive sea use. Ecological response, including the biome structure index, the structure and function index of ecological sensitive area, reflects the ecological response of the different trophic levels to environment changes resulted from the intensive use sea. The evaluation index system is well arranged, which can comprehensively and objectively reflect the characteristics, state changes and influence degree of different level subsystems of ecosystem. Connecting with our country's marine environmental monitoring and current assessment, the weight, standard and evaluation grade of ecological impact factors were studied and determined. The model based on comprehensive index method was also established, which may evaluate the impacts of the intensive sea use on marine ecology, and thus determine the suitability of marine engineering proposal using the variation of the sea ecological environment comprehensive index before and after the project construction of the intensive use sea (ΔE). When ΔE > 30%, it implies that marine ecosystem suffers severely impact; when 15% < ΔE≤30%, it suggests that marine ecosystem suffers large impact; when 5% < ΔE≤15%, it suggests that marine ecosystem suffers general impact; and when ΔE≤5%, it indicates that marine ecosystem is slight affected or not affected. Therefore, these results are expected to offer appropriate technological supports for deciding the scales and sites of the intensive marine engineerings, and also provide service for scientific management of the intensive sea use.