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The integration of flexible structures into conventional rigid systems significantly enhances such systems’ mobility in complex environments, enabling greater adaptability and morphological reconfigurability. However, introducing flexible structures greatly increases system complexity, resulting in highly nonlinear, time-varying, and strongly coupled dynamics that pose substantial challenges for accurate modeling and control design. In this paper, we investigate the dynamic modeling of a modular worm-like hybrid robot that integrates both rigid and flexible components. The robot features two locomotion modes: a worm-like gait mode and a modular mode where each unit operates independently, akin to small AGVs. Using this robot as a representative platform, we construct a Lagrangian-based dynamic model that incorporates structural flexibility through rigid–flexible coupling, while also accounting for actuation and contact interactions. In rotational tasks, the proposed model achieves significantly improved accuracy by accounting for structural flexibility, while both models exhibit comparable behavior during linear locomotion. These results highlight the model’s enhanced fidelity in capturing the dynamics of flexible modular systems. This modeling framework offers a practical basis for more accurate simulation, control system development, and performance analysis of decentralized rigid–flexible robotic platforms.