Production system flexibility has become an important factor to meet the needs of diversified markets in an ever-changing and turbulent market environment. Thus, this paper addresses the problems of flexibility evaluation for decision making by evaluation method driven by digital twin, which models, predicts, and evaluates the flexibility of a given production system design scheme (PSDS). Based on the definition and characteristic analysis of flexibility in the production system design phase, and combined with data modelling (static function model (SFM) and dynamic prediction model (DPM)) and data analysis (AHP-based and simulation-based analysis), the proposed framework evaluates system flexibility from the static and dynamic levels, helps enterprises quickly obtain the system’s comprehensive flexibility evaluation index, realizing the rapid screening of the production system design scheme (PSDS). The successful application of the evaluation framework in case enterprise has fully proved the feasibility and effectiveness of the method.