The decision-making trial and evaluation laboratory (DEMATEL) method has been widely applied to identifying critical factors of simple systems in different fields. Although lots of efforts have been spent on improving the DEMATEL, they are still suitable for simple systems but cannot solve the decision problems in complex systems. This study focuses on providing a hierarchical DEMATEL method for the complex systems with numerous system factors, multiple types of influences, and the existence of hierarchy. The hierarchical decomposition is firstly introduced to provide an analytic framework for simplifying the DEMATEL problem of complex systems, in which the horizontal decomposition deals with multiple types of influences and the vertical decomposition deals with the existence of hierarchy and numerous system factors. Then a direct influence analysis is proposed to construct initial direct-relation (IDR) matrices for the elements within each subsystem, and a super IDR matrix is defined and constructed by integrating the IDR matrices on all pairs of subsystems at the levels from the lowest to the highest recursively. The hierarchical DEMATEL method with three algorithms is established for identifying critical factors by means of taking the super IDR matrix for multi-level subsystem structure into the procedure of DEMATEL. Finally, two illustrative examples are proposed to discuss the superiority of the proposed method and its algorithms.