Combat system effectiveness simulation (CSES) is a special type of complex system simulation. Three non-functional requirements (NFRs), i.e. model composability, domain specific modeling, and model evolvability, are gaining higher priority from CSES users when evaluating different modeling methodologies for CSES. Traditional CSES modeling methodologies are either domain-neutral (lack of domain characteristics consideration and limited support for model composability) or domain-oriented (lack of openness and evolvability) and fall short of the three NFRs. Inspired by the concept of architecture in systems engineering and software engineering fields, we extend it into a concept of model architecture for complex simulation systems, and propose a model architecture-oriented modeling methodology in which the model architecture plays a central role in achieving the three NFRs. Various model-driven engineering (MDE) approaches and technologies, including simulation modeling platform (SMP), unified modeling language (UML), domain specific modeling (DSM), eclipse modeling framework (EMF), graphical modeling framework (GMF), and so forth, are applied where possible in representing the CSES model architecture and its components’ behaviors from physical and cognitive domain aspects. A prototype CSES system, called weapon effectiveness simulation system (WESS), and a non-trivial air-combat simulation example are presented to demonstrate the methodology.