With the application of public–private partnership (PPP) model in urban transportation infrastructure projects, various participants have put forward multi-dimensional demands to the operation and maintenance of infrastructures. This study aims to establish a systematic operational performance evaluation framework for PPP transportation infrastructure projects. Based on a literature review, the balanced scorecard was improved, and a conceptual model of multidimensional performance assessment was constructed. The structure of the qualitative performance assessment system was quantified and analyzed by combining structural equation modeling with questionnaires to obtain causal relationships among the indicators. Subsequently, a system dynamics model was constructed to assess the performance dynamically, and a validation analysis was conducted. It finds that maintaining a low level of operational quality over an extended period can significantly reduce stakeholder satisfaction, consequently exacerbating the decline in project performance. In contrast, an improvement in the level of informatization is found to positively contribute to enhancing operational quality and facilitating the long-term sustainability of project operations. It innovatively integrates four dimensions of financial, multi-stakeholder satisfaction, operation and maintenance quality, and sustainability performance to enrich the theoretical system of PPP transportation infrastructure performance assessment. At the same time, it analyzes the influence mechanism among the indicators and its long-term dynamic performance, which provides an effective decision-making tool for operational performance management.