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Seismic mitigation of transportation systems has become a worldwide challenge, because identifying an optimal retrofit strategy entails significant computational efforts, especially for large-scale networks with numerous candidate strategies and time-consuming risk assessment processes. An efficient joint importance-based methodology is proposed in this paper to address the challenge. The proposed method selects the component set (e.g., bridges) that is most decisive to the network seismic risk based on only one set of stochastic samples but takes into account the uncertainty of multiple damage states and the interactive effect between different components. The reliability and stability of the proposed method are verified on a hypothetical transportation network under different conditions.