Following the basic organization hierarchy of biology, eco-agricultural models can be classified into the following fundamental classes: landscape model (at landscape level), in which agricultural land arrangement pattern is essential; cycling model (at ecosystem level), in which the core model is linked to different compartments of agro-ecosystems through energy and material flow; vertical model (at community level), in which structural arrangement of species is important; food-chain model (at population level), which relates to the structural design of food-chain; and variety structure model (at individual and gene level), which relates to the choice of plant and animal species. Models in upper levels interact with models in lower level forming a complex system. This fundamental classification of eco-agricultural models does not rule out other methods of classification for specific purposes but it provides understanding and enhances analysis of other classification methods. This fundamental classification benefits identification of important developmental processes of eco-agriculture. It also benefits the improvement, selection, standardization and research on eco-agricultural models.