From the perspective of energy efficiency and environmental sustainability, the scheduling problem in a flexible workshop with the utilization of automated guided vehicles (AGVs) was investigated for material transportation. Addressing the dual-constrained integrated scheduling challenge involving machining machines and AGVs, a scheduling optimization model was established with makespan, workshop energy consumption, and processing quality as the optimization objectives. To effectively solve this model, an enhanced whale optimization algorithm (IWOA) was proposed. Specifically, nonlinear convergence factors, adaptive inertia weights, and improved helix positions were introduced into the standard whale optimization algorithm to update the model. Furthermore, a loss function was constructed based on fuzzy membership theory to obtain the optimal compromise solution of the multi-objective model. The research results indicate that: (1) The IWOA obtained the optimal solutions on benchmark instances MK01, MK02, MK04, MK07, and MK08; (2) The IWOA outperformed the WOA(1), WOA(2), WOA-LEDE, and NSGA-II algorithms in the two instances provided in this paper, demonstrating strong robustness of the model; (3) Although the multi-objective model constructed in this paper could not surpass the single-objective optimal solution in individual objectives, it achieved compensation in other objectives, effectively balancing the trade-offs among the makespan, workshop energy consumption, and processing quality of the three objectives. This research offers an effective practical approach to address green flexible workshop scheduling with AGV transportation.