Energy-saving scheduling is a well-known issue in the manufacturing system. The flexibility of the workshop increases the difficulty of scheduling. In the workshop schedule, considering the collaborative optimization of multi-level structure product production and energy consumption has certain practical significance. The process sequence of parts and components should be consistent with the assembly sequence. Additionally, the non-production energy consumption (NPEC) (such as the energy consumption of workpiece handling, equipment standby, and workpiece conversion) generated by the auxiliary machining operations, which make up the majority of the total energy consumption, should not be ignored. A sub-batch priority is set according to the upper and lower coupling relationship in the product structure. A bi-objective batch scheduling model that minimizes the total energy consumption and the total completion time is developed, and the multi-objective gray wolf optimizer (MOGWO) is employed as the solution to obtain the optimal schedule scheme. A case study is performed to demonstrate the potential possibilities concerning NPEC in regard to reducing the total energy consumption and to show the effectiveness of the algorithm. Compared with the traditional optimization model, the joint optimization of NPEC and PEC can reduce the energy consumption of standby and handling by 9.95% and 22.28%, respectively.