Abstract Complex systems are commonly composed of interconnected and inter‐ and intradependent subsystems, which in their essence constitute systems of systems with multiple functions, operations, and stakeholders. Phantom System Models (PSM) is a modeling methodology inspired by philosophical and conceptual thinking from the arts, and is driven and supported by systems engineering theory, methodology, and practice. The PSM is designed to model inter‐ and intradependencies between and among the subsystems of a complex system of systems by exploiting vital knowledge and information embedded in the intrinsic and extrinsic common and uncommon state variables among the subsystems. Among the several systems engineering theories and methodologies, the PSM in particular builds on the centrality of the states of the system in modeling and in risk analysis; fundamentals in system identification (the inverse problem); hierarchical holographic modeling; coordinated hierarchical Bayesian model; and hierarchical decomposition and higher‐level coordination. An example problem of a PSM‐based modeling of a prototype system of systems is presented. © 2012 Wiley Periodicals, Inc. Syst Eng