This paper describes a new methodology for analyzing organisational innovation and deviation phenomena by combination of agent based simulation and case design. Organisational deviation is inextricably linked to innovation, because they are activities in business firms to break standards in operations. However, it is assumed that the former and the latter are different in terms of external utilities. Under the assumptions, we have developed a unified agent based model and have made simulation for analyzing the emergence process of innovation and deviation. The simulation results are confirmed through manual simulation and case analysis in order to obtain an in-depth understanding of inextricably linked organisational phenomena, and to distinguish the similarities and differences between innovation and deviation.