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This invention discloses a distributed heterogeneous flexible assembly workshop scheduling method with transfer functionality. It includes the following steps: setting assumptions and basic parameters; proposing corresponding constraints based on the problem under study; constructing a bi-objective optimization model with the objectives of minimizing maximum completion time and minimizing total processing energy consumption. This bi-objective optimization model is used to optimize the flexible assembly workshop scheduling considering factory processing capacity, transportation stages, and workpiece transfer. Based on the process sequence, factory selection, and machine selection, a three-segment encoding and decoding mode corresponding to the bi-objective optimization model is designed. Based on the three-segment encoding and decoding modes, an improved multi-objective genetic algorithm based on Q-Learning is used to solve for the optimal scheduling scheme. This invention considers factors such as workshop processing capacity, collaborative processing, and transportation stage time, arranging the process sequence, factory, machine, and assembly workshop selection from a global optimization perspective.