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This paper considers a federation-based pragmatic integration framework of heterogeneous information systems multi-objective integration for not-long-term-stable inter-connection, inter-communication and inter-operation under the condition of control domain and trust domain incomplete coverage. A prototyping system has been designed and developed in order to verify the validity of this framework. In comparison with existing integration methods, the real cooperation individuals of collaboration need not be themselves,but also projections on given interested domains. And collaborations exist in two levels: physical level and logical level, they are respectively settled in the scope of system federation and application federation. A federation-based collaborative design-simulation optimization system is explored in this paper to demonstrate the practicality of our framework.