Disturbances undergone by a complex system can come as much from its external environment as from the internal elements which constitute it. Complex systems are understood in this study as composed of intelligent machines and humans (IMH), and being in charge to accomplish complex tasks in a collaborative way. Performances of these systems, in terms of robustness, adaptation and resilience, strongly depend on the behaviour of the IMH duo. The works that are the subject of this paper focus on the study of the IMH duo and propose a methodological process using jointly cognitive approaches with formal modelling and simulation to analyse, design and control complex systems. For those systems, human beings are necessarily implied in their global behaviour –including stability–, what crucially calls for a better understanding of their behaviour facing diverse complex situations: normal situations, risky situations, critical and accidental situations. Tools and methods proposed by cognitive Sciences, Cognitive Engineering and Knowledge Engineering allow to take into account the different mechanisms involved in human behaviour to enrich complex system models for a better design and control to munimize human errors.