Complex dynamical networks consisting of many components that interact and produce each other are difficult to understand, especially, when new components may appear. In this paper we outline a theory to deal with such systems. The theory consists of two parts. The first part introduces the concept of a chemical organisation as a closed and self-maintaining set of components. This concept allows to map a complex (reaction) network to the set of organisations, providing a new view on the system’s structure. The second part connects dynamics with the set of organisations, which allows to map a movement of the system in state space to a movement in the set of organisations.