This paper proposes a Behaviour Prediction Framework with an objective to help designers tackling the problem of uncertainty emerging from system architecture and the effects of the uncertain operating conditions. The proposed framework combines structural and dynamic system model. The Design Structure Matrix is applied to model structural arrangements and dependencies between the subsystems. The Model Predictive Control is applied to model the system in discrete and continuous dynamic domains. As the result of the proposed framework, stability analysis of subsystems in interaction become possible and feedback on system architecture could be provided. To test validity of the proposed approach, the test case involving climate chamber with heat regeneration is presented.