Ship painting, as one of the three pillars of the shipping industry, runs through the whole process of ship construction. However, there are low scheduling efficiency and excessive carbon emissions in the segmental painting process, and optimizing the scheduling method is an important means to achieve the sustainable development of the ship manufacturing industry. To this end, firstly, a low-carbon scheduling mathematical model for the segmented painting workshop is proposed, aiming to reduce carbon emissions and improve the painting efficiency of the segmented painting workshop. Second, an artificial bee colony algorithm designed based on a decomposition strategy (MD/ABC) is proposed to solve the model. In the first stage, five neighborhood switching methods are designed to achieve the global search employed for each solution. In the second stage, the Technique of Ordering the Ideal Solutions (TOPSIS) improves the competition mechanism through the co-evolution between neighboring subproblems and designs the angle to define the relationship between neighboring subproblems to enhance the localized search and improve population quality. The solution exchange strategy is used in the third stage to improve the efficiency of the algorithm. In addition, a two-stage coding method is designed according to the characteristics of the scheduling problem. Finally, the algorithm before and after the improvement and with other algorithms is analyzed using comparative numerical experiments. The experimental results show the effectiveness of the algorithm in solving the low-carbon scheduling problem of ship segmental painting and can provide reliable guidance for the scheduling program of segmented painting workshops in shipyards.