Abstract: Because the definitions of the core concepts and theories of ecology, such as community, ecosystem, etc., are operational, they are not clearly defined, which can easily lead to ambiguities and terminological confusion among different users and ecological situations.Meanwhile some ecological theories, for example, theories about community succession, ecological balance, diversity and stability, cannot effectively realize the ontological commitment to these ecological entities, phenomena,and processes. There existed divergences between holism and reductionism, realism and anti-realism in ecology. A holon spanning all structural and functional levels of the ecosystem, whose variable quantity and constant essential relationship between whole and part, may provide us with new enlightenment to solve the ecological ontological problems.