Increasing marine engineering projects have resulted in ecological degradation of fishery resources. In this study, combining survey data, historical data, data from fishermen's interviews, and many other data, we focused on the core issue of compensation for damage to fishery resources due to marine engineering projects. The survey data were obtained from 80 stations in the coastal waters of Zhoushan (29°20'-31°00'N, 121°40'-123°00'E), collected between November 2015 and May 2016. Different aquatic areas, fishery production areas or spawning and egg gathering areas, and areas endowed with different fishery resources were assigned various weighting coefficients in the compensation model, including direct economic damage compensation and indirect ecological damage compensation for reclamation projects. Standard techniques were used for the calculation of ecological damage to fishery resources in the coastal waters of different counties (districts) and townships along nearshore Zhoushan. The developed compensation model not only offers useful application in the collection of compensation for ecological damage to fishery resources in the coastal waters near Zhoushan, but also provides technical support for establishing compensation mechanisms for marine ecological damage in China.