Heat loss is an important loss in the manufacturing process, which has a significant impact on the overall system performance and resource utilization efficiency. Therefore, optimizing heat loss can not only improve manufacturing efficiency, but also promote the green transformation of enterprises. The purpose of this paper is to explore the green unit scheduling and performance management strategy of manufacturing system based on heat loss optimization, so as to improve the energy efficiency and overall performance of manufacturing system. A new scheduling model is proposed, which combines heat loss analysis with green management strategy. By using multi-objective optimization algorithm, the scheduling of manufacturing cells is optimized, focusing on the minimization of heat loss and the maximization of production efficiency. The thermal energy loss characteristics of each process and the operating state of the equipment are considered in the model, and the energy efficiency performance of different scheduling schemes is verified by simulation experiments. The experimental results show that the optimized scheduling scheme significantly reduces the thermal energy loss of the manufacturing system, significantly improves the overall production efficiency, and effectively improves the green performance indicators, including the reduction of energy consumption and waste emission. Through the scheduling and management strategy based on the optimization of heat loss, the green production goal of the manufacturing system is realized. The research of this paper provides a new idea and method for manufacturing enterprises to realize sustainable development while pursuing economic benefit.