The scheduling of tower crane operations is a complex process. Overlapping areas between tower cranes often lead to increased collision possibilities, resulting in additional tower crane operation complexity. Single objectives related to time or economic aspects were always considered in dealing with this issue, which neglected other objectives and the relationships between different objectives. Therefore, this article proposes a novel method for the schedule of prefabricated component lifting tasks on the construction site, integrating the multi-objective optimization model with the decision-making method with the aim of minimizing energy consumption costs and minimizing the amplitude of the costs among multiple tower cranes. A non-dominated sorting genetic algorithm-III (NSGA-III) written in Python is used as the multi-objective optimization algorithm—which considers the selection of tasks for each tower crane and the order of lifting for each tower crane and technique for order preference by similarity to an ideal solution (TOPSIS), and is applied as the decision-making method for ranking the Pareto front. Then, a green construction production and education integration training building construction project located in Jinan, China is used as the case study to verify that the method is practical and reasonable. The results show that conflicts can be effectively avoided, energy consumption costs reduced, and equipment utilization increased by rationally distributing lifting tasks among multiple overlapping tower cranes. And among the top 11 solutions, the lifting tasks and priorities for tower crane 1 are close to the same. In contrast, the task lifting for tower crane 2 was assigned based on the balance of the energy consumption costs of the two tower cranes. The discovery of this article is helpful to eliminate collisions, interference, and frequent start and stop of several tower cranes, so as to realize the safe, stable, and efficient operation of the construction site.