According to characters of marine ecology domain knowledge, a marine ecology knowledge organization model was proposed. Referring to engineering field literature and the device-function knowledge representation theory that the "function" concept was used to describe marine ecology functional process; a viewpoint of device-function was fixed, a domain upper ontology for marine ecosystem was presented, and then marine ecological conceptual model and marine ecology OWL ontology were constructed. By extending OWL-DL, OWL-Process model oriented function-process was proposed, and then marine ecology function-process ontology instance was constructed. Based on constructed marine ecology ontology repository, marine ecological knowledge management system was developed. The ontology application system provides marine ecology knowledge query and crisis early warning functions; and it also verifies the validity, rationality and feasibility of constructed marine ecology ontology.