Due to the complexity of business ecosystems, the architecture of business ecosystems has not been well discussed in the literature, and modeling or simulation of business ecosystems has been rarely focused. Therefore, this paper proposes a business ecosystem ontology and introduces a methodology for business ecosystem architecture design. The proposed methodology includes five stages: 1) Boundary identification of a business ecosystem; 2) Identification of actors and their roles in the business ecosystem; 3) Identification of actors’ value propositions; 4) Identification of interaction between actors; 5) Verification of business ecosystem architecture design. This paper uses the Danish electricity system as an example to introduce the methodology, and use Electric Vehicle home charging as a case study to demonstrate the application of the developed methodology. The case study demonstrates that the proposed methodology is a systematic approach and can be easily applied to any ecosystem architecture design with the five stages, and the designed ecosystem architecture can represent the physical system and business. Several definitions are clarified in the paper, e.g., actor, role, interaction, ecosystem roadmap and expanded/shifted ecosystem, etc. With clear definitions, the proposed methodology provides a visualized, clear structure of behaviors and specifications for a given business ecosystem.