Abstract: This paper introduces the application of compensation method for ecological loss caused by Marine engineering construction from two aspects: financial compensation and ecological restoration compensation. Two methods of ecological loss compensation fund accounting are discussed in the part of financial compensation, based on the ecosystem service function and based on the ecological restoration respectively. Ecological restoration compensation mainly introduces two different ways: the in situ ecological restoration compensation of structural forms with ecological effects from the engineering structure itself, and the heterotopic ecological restoration compensation of constructing new habitats in other places for ecological reconstruction. Last the compensation scale of different marine engineering is estimated based on HEA.