China faces significant environmental challenges, including reducing pollutants, improving environmental quality, and peaking carbon emissions. Industrial restructuring is key to achieving both emission reductions and economic transformation. This study uses the Environmentally Extended Multi-Regional Input-Output model and multi-objective optimization to analyze pathways for China’s industrial transformation to synergistically reduce emissions. Our findings indicate that under a compromise scenario, China’s carbon emissions could stabilize at around 10.9 billion tonnes by 2030, with energy consumption controlled at approximately 5 billion tonnes. The Papermaking sector in Guangdong and the Chemicals sector in Shandong are expected to flourish, while the Coal Mining sector in Shanxi and the Communication Equipment sector in Jiangsu will see reductions. The synergy strength between carbon emission reduction and energy conservation is highest at 11%, followed by a 7% synergy between carbon emission and nitrogen oxide reduction. However, significant trade-offs are observed between carbon emission reduction and chemical oxygen demand, and ammonia nitrogen reduction targets at -9%. This comprehensive analysis at regional and sectoral levels provides valuable insights for advancing China’s carbon reduction and pollution control goals.