Organized complexity is a characteristic feature of ecological systems with heterogeneous components interacting at several spatio-temporal scales. The hierarchy theory is a powerful epistemological framework to describe such systems by decomposing them vertically into levels and horizontally into holons. It was at first developed in a temporal and functional perspective and then, in the context of landscape ecology, extended to a spatial and structural approach. So far, most ecological applications of this theory were restricted to observational purposes, using multi-scale analysis to describe hierarchies. In spite of an increasing attention to dynamics of hierarchically structured ecological systems, current simulation models are still very limited in their representation of self-organization in complex adaptive systems. An ontological conceptualization of the hierarchy theory is outlined, focusing on key concepts, such as levels of organization and the compound and component faces of the holons. Various existing formalisms are currently used in simulation modelling, such as system dynamics, discrete event and agent based paradigms. Their ability to express the hierarchical organization of dynamical ecological systems is discussed. It turns out that a multi-modelling approach linking all these formalisms and oriented toward the specification of a constructive dynamical system would be able to express the dynamical structure of the hierarchy (creation, destruction and change of holons) and the functional and structural links between levels of organization.