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The reconfiguration process, i.e. the layout adjustment, of a reconfigurable material handling system (RMHS) plays an important role in the planning of a reconfigurable manufacturing system (RMS). This paper gives a new definition of RMHS, and presents a novel method based on graph theory and logic calculus for configuration modelling of a robot-based RMHS. The method is developed with full consideration of the reconfigurablility of robot and the system respectively at machine-level and system-level. To tackle the reconfiguration problem of a RMHS, an indirect method including two stages is developed. Firstly according to the material handling task, the optional configurations can be deducted by adopting first-order logic calculus. Secondly the discrete dynamic programming with a novel stage partition strategy is investigated to select appropriate configurations for the completion of the reconfiguration process of the RMHS. Numerical study demonstrates that the robot-based RMHS of practical sizes can be effectively and rapidly reconfigured to accommodate transportation changes.