This paper proposes a methodology for modeling interoperability in a context of collaborative Supply Chain Networks. The purpose of the study is to develop a methodology that enables: (1) the design of collaborative Supply Chain Network platforms that are able to deliver a high degree of business interoperability in the implementation of collaborative Supply Chain Network management practices; and (2) the analysis of the impact of business interoperability on the performance of collaborative organizations that are involved in the implementation of those management practices. The design of the Supply Chain Network platforms is grounded on the Axiomatic Design Theory and the analysis of the impact is grounded on the Agent-based Simulation. A theoretical axiomatic design model and a theoretical agent-based simulation model are proposed. The proposed methodology is demonstrated through an application scenario to implement Reverse Logistics in a context of automotive industry. The results show that this methodology is a good starting point for a more comprehensive framework towards interoperable Supply Chain Network modelling.