Energy and resource efficiency, as main instruments of sustainability, have become important objectives for industrial companies. Innovative tools and methods are needed to design sustainable, energy and resource efficient systems and processes of a factory. Against this background, the “Method for Factory System Modeling in the Context of Energy and Resource Efficiency” (FSMER) has been developed and evaluated. The method FSMER consists of a Meta Model, four comprehensive Factory System Concepts for the description of hierarchy, function, structure and life cycle, a Reference Model and a Procedure Model. The method aims at the holistic, methodical and model-based description of the factory in order to consider the objectives energy and resource efficiency in early conceptual planning phases. In addition, interrelationships are explained and potentials for efficiency improvements are identified. Therefore, FSMER supports the representation and evaluation of the complex factory system in a simplified and graphical form. By this, effects of planning decisions can also be visualized. In the paper, the method and its evaluation are described.