Abstract Cyber-physical systems (CPSs) are used in many safety-critical areas, making it crucial to ensure their safety. However, with CPSs increasingly dynamically deployed and reconfigured during runtime, their safety analysis becomes challenging. For one thing, reconfigurable CPSs usually consist of multiple agents dynamically connected during runtime. Their highly dynamic system topologies are too intricate for traditional modeling languages, which, in turn, hinders formal analysis. For another, due to the growing size and uncertainty of reconfigurable CPSs, their system models can be huge and even unavailable at design time. This calls for runtime analysis approaches with better scalability and efficiency. To address these challenges, we propose a scenario-based hierarchical modeling language for reconfigurable CPS. It provides template models for agent inherent features, together with an instantiation mechanism to activate single agent’s runtime behavior, communication configurations for multiple agents’ connected behaviors, and scenario task configurations for their dynamic topologies. We also present a path-oriented falsification approach to falsify system requirements. It employs classification-model-based optimization to explore search space effectively and cut unnecessary system simulations and robustness calculations for efficiency. Our modeling and falsification are implemented in a tool called . Experiments have shown that it can largely reduce modeling time and improve modeling accuracy, and perform scalable CPS falsification with high success rates in seconds.