AbstractA hybrid flow shop is pivotal in modern manufacturing systems, where various emergencies and disturbances occur within the smart manufacturing context. Efficiently solving the dynamic hybrid flow shop scheduling problem (HFSP), characterised by dynamic release times, uncertain job processing times, and flexible machine maintenance has become a significant research focus. A NeuroEvolution of Augmenting Topologies (NEAT) algorithm is proposed to minimise the maximum completion time. To improve the NEAT algorithm's efficiency and effectiveness, several features were integrated: a multi‐agent system with autonomous interaction and centralised training to develop the parallel machine scheduling policy, a maintenance‐related scheduling action for optimal maintenance decision learning, and a proactive scheduling action to avoid waiting for jobs at decision moments, thereby exploring a broader solution space. The performance of the trained NEAT model was experimentally compared with the Deep Q‐Network (DQN) and five classical priority dispatching rules (PDRs) across various problem scales. The results show that the NEAT algorithm achieves better solutions and responds more quickly to dynamic changes than DQN and PDRs. Furthermore, generalisation test results demonstrate NEAT's rapid problem‐solving ability on test instances different from the training set.