A crucial measure to accelerate the low-carbon transformation of enterprises in the industrial sector involves stringent control over carbon emissions attributed to logistics and transportation activities. In this study, a multi-objective workshop layout optimization model is developed, aiming to minimize logistics cost per unit area and carbon emissions, and maximize the non-logistics relationship. The objective is to mitigate avoidable transportation-related carbon emissions during enterprise operations, while facilitating the co-development of the enterprise’s economy and environment. The model is solved utilizing an enhanced NSGA-II algorithm, with the initial solution set optimized through a combination of system layout design method, dynamic adaptive crossover, and variation strategies. Additionally, the distribution function is introduced to enhance the elite retention strategy and boost the algorithm’s search rate. By using an actual case study, the usefulness of the enhanced algorithm is demonstrated, and the plant’s initial low-carbon layout is realized in order to advance the enterprises’ sustainable growth.