Under the background of the Internet of things (IoT), the problems between the actual production and the environment are also prominent. The environmental cost control in the production process of manufacturing enterprises are discussed to reduce the environmental cost and promote the improvement of production efficiency. First, the environmental cost under the background of IoT is analyzed. Also, the environmental cost control methods in the production process of traditional manufacturing enterprises are investigated. Second, based on the principle of traditional genetic algorithm, the fast-nondominated sorting genetic algorithm (NSGA-II) of multiobjective genetic algorithm is introduced to complete the optimization of BP neural network (BPNN) algorithm in deep learning (DL), and the multiobjective GA optimization BPNN model is established. Finally, the multiobjective GA algorithm is used to empirically analyze the environmental cost control capability of a paper-making enterprise. It is compared with enterprises with excellent and poor environmental cost control capabilities in the same industry to find out secondary indexes. The results show that environmental costs have long-term and economic characteristics. The global search ability of BPNN optimized by multiobjective GA is improved, and the local optimal dilemma is avoided. Through empirical analysis, it is found that the comprehensive capability of the environmental cost control of the enterprise is better, scored 79 or more, and the indexes of insufficient development and advantages are obtained. As IoT rapidly develops, it is necessary to further improve the ability of enterprises in environmental cost management, which is very important to promote the development of enterprises and enhance their core competitiveness. It is hoped that this investigation can provide certain reference significance for improving the environmental cost management capability of enterprises, increasing production efficiency, and reducing environmental costs.