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There are few topics more heated than the discussion surrounding open source software versus commercial and proprietary software. They are not only in an opposite relation, but also looking for cooperation. Moreover, there are many unresolved problems between them, in which the most typical one is the interoperability. There is a real need for a widely adopted, standardized method to assess the interoperability of open source software. However, few groups or researchers have given the guide up to now. This paper proposed Bayesian Network to construct the structure of interoperability and then learn the condition probability table of the structure. The structure and its condition probability table constitute the interoperability model. The model can be used not only to help user evaluate the interoperability of open source software, but also to guide the software developer to improve the quality of open source software more efficiently. An application showed how to use the model, and the result proved the validity of this model.