This article describes an architecture flow optimization (AFO) method for naval ship System design. AFO is a network-based method. It is used to design and analyze naval ship Mission, Power, and Energy Systems (MPES) in a naval ship Concept and Requirements Exploration (C&RE) process at a sufficient level of detail to better understand system energy flow, define MPES architecture and sizing, reduce system vulnerability, and improve system reliability. This method decomposes MPES into three architectures: logical, physical, and operational which describe the system’s spatial, functional, and temporal characteristics, respectively. Using this framework, the AFO incorporates system topologies, input/output energy coefficient component models, preliminary arrangements, and (nominal and damaged) steady-state operational scenarios into a linear optimization method to minimize the energy flow cost required to satisfy all operational scenario demands and constraints. AFO results are used to inform system topology design and assess the feasibly and survivability of representative designs in the C&RE process. AFO results may also be used in physics-based vital component sizing, calculation of vulnerability/effectiveness metrics in the C&RE process, and subsequent linear optimization formulations to assess recoverability and operational effectiveness in the time domain.