The exploration of component states for optimizing maintenance schedules in complex systems has garnered significant interest from researchers. However, current literature usually overlooks the critical aspects of system flexibility and reconfigurability. Judicious implementation of system reconfiguration can effectively mitigate system downtime and enhance production continuity. This study proposes a dynamic condition-based maintenance policy considering reconfiguration for reconfigurable systems. A double-layer decision rule was constructed for the devices and systems. To achieve the best overall maintenance effect of the system, the remaining useful life probability distribution and recommended maintenance time of each device were used to optimize the concurrent maintenance time window of the devices and determine whether to reconfigure them. A comprehensive maintenance efficiency index was introduced that simultaneously considered the maintenance cost rate, reliability, and availability of the system to characterize the overall maintenance effect. The reconfiguration cost was included in the maintenance cost. The proposed policy was tested through numerical experiments and compared with different-level policies. The results show that the proposed policy can significantly reduce the downtime and maintenance costs and improve the overall system reliability and availability.