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Complex systems are prevalent in nature and man-made world. Modelling plays an important role in studying the dynamics of complex systems which are often characterised by collective behaviour that cannot be determined from investigating its parts in isolation. Complex systems modelling involves use of cross-disciplinary theories and methods and a variety of approaches have been proposed to this end, such as system dynamics modelling, agent based modelling, graph-based modelling and so on. Due to the inherent complexity, most of the modelling approaches rely on human intervention and input from subject matter experts to develop models. This project will focus on research and development of computational intelligence based methods and processes that can substitute manual processes in complex system modelling in order to minimise expert reliance. The main aim of this research is to simplify, streamline and minimise error, bias, time and effort in model development through this automation. Specifically, this research will apply the automated methods to the modelling of capability systems which are perfect instances of engineered complex systems.