In this study, we present and discuss a variant of the classical vehicle routing problem (VRP), namely the heterogeneous multitype fleet green automated guided vehicle (AGV) routing problem with time windows (HFGVRPTW) applied in the workshops of flexible manufacturing systems (FMS). Specifically, based on the analysis of AGV body structure and motion state, transport distance and energy consumption are selected as two optimization objectives. According to the characteristics and application context of the problem, this paper designs a hybrid genetic algorithm with large neighborhood search (GA-LNS) considering the farthest insertion heuristic. GA-LNS is improved by increasing the local search ability of genetic algorithm to enhance the solution optimal quality. Extensive computational experiments which are generated from Solomon’s benchmark instances and a real case of FMS are designed to evaluate and demonstrate the efficiency and effectiveness of the proposed model and algorithm. The experimental results reveal that compared with using the traditional homogeneous fleet, the heterogeneous multitype AGV fleet transportation mode has a huge energy-saving potential in workshop intralogistics.