According to the marine ecology classification method, a marine organism environment area is divided into two scenes and four components; the two scenes comprise a biological geographic scene classification unit and an aquatic scene classification unit, and the four components comprise a water body component classification unit, a landform component classification unit, a substrate component classification unit and a biological component classification unit. The water body component classification unit is divided into five sub-components including a water layer, temperature, salinity, hydrological morphology and biogeochemical characteristics; the landform component classification unit is divided into four sub-components including a structural landform, a geographical environment landform, a first-level landform and a second-level landform; the substrate component classification unit comprises a substrate large class, a substrate class, a substrate subclass, a substrate group and a substrate subgroup; the biological component classification unit comprises biological large classes, biological classes, biological subclasses, biological groups and biological communities. According to the invention, various kinds of ocean data can be integrated under a unified ecological framework, mapping application can be carried out, and spatialized natural resource management based on an ocean ecological system is supported.