The manufacturing industry is the pillar industry of China’s economy and a major carbon emitter, and its carbon emission reduction efforts directly determine whether the country’s carbon emission reduction target can be successfully met. In the context of the goals of the carbon peak and carbon neutrality policy, we examine the impact of manufacturing structure optimization on carbon emissions from 2003 to 2020 through a spatial econometric model, taking the old industrial centers in Northeast China as an example. We then apply a machine learning model to simulate manufacturing carbon emissions during the carbon peak stage and identify the optimal path for carbon emission reduction, which is important for promoting manufacturing carbon emission reduction in Northeast China. Since the goal of low-carbon economic development has gradually replaced the goal of maximizing economic efficiency in recent years, manufacturing structure optimization has come to focus on energy saving and emission reduction. Therefore, we define manufacturing structure optimization from the dual perspective of technology and energy consumption to broaden the existing research perspective. The results show the following: (1) The overall trend in manufacturing structure optimization in Northeast China is steadily improving, and the level of manufacturing structure optimization from the technology perspective is higher than that from the energy consumption perspective. (2) Manufacturing structure optimization and manufacturing carbon emissions in Northeast China both show a positive spatial correlation. Manufacturing structure optimization in Northeast China can effectively promote carbon emission reduction, and it also has a spatial spillover effect. (3) The carbon emission reduction effect of manufacturing structure optimization from the energy consumption perspective is better than that from the technology perspective, and the carbon emission reduction effect under the institutional innovation scenario is better than that under the baseline scenario and the technological innovation scenario. Focusing on manufacturing structure optimization from both technology and energy consumption perspectives, as well as continuously improving technological innovation and institutional innovation, can help to achieve manufacturing carbon emission reduction in Northeast China.