Modern process system can be regarded as multi-medium interacted heterogeneous networks comprised of material transportation, power supply and control information exchange, in which substance like material, energy and information coexist and interact. Thus fault diagnosis and safety analysis for complex process system based on homogeneous network theory should be improved to hold multi-medium interacted property. This paper proposed a new modeling approach for multi-medium interacted heterogeneous networks of complex process system based on polychromatic sets theory. Multi-mediums of process system and their interacted relation are described in polychromatic sets and contour matrixes. The topology structure of process system networks in polychromatic sets description is converted into unified hierarchical formal model which can be conveniently expressed in logical operation form. The unified hierarchical formal model developed in this method for multi-medium interacted heterogeneous networks of complex process system has concise form and contains more information than homogeneous network description. This makes fault diagnosis and safety analysis based on networks theory more effective and complete.