Carbon dioxide peaking and carbon neutrality, a grand strategic goal in China, is of great significance to promoting eco-transformation and green development of the manufacturing industry. Achieving decoupling of economic growth with resource-energy consumption and pollutants-carbon dioxide emissions will underpin the goal substantially. The coastal regions in China, driven by the manufacturing industry, have been well developed but also witnessed intensive pollutants and carbon dioxide emissions. Thus, synergizing the reduction of pollutants and carbon dioxide emissions has great practical significance for regional eco-transformation. Taking Ningbo City in the Zhejiang Province as a case study, this article conducts empirical research on the industrial structure adjustment of two-digital level industries by establishing a multi-criteria decision-making model under different scenarios. The model takes energy, water resources, four main pollutants, and carbon dioxide as constraints, and the degree of change in the proportion of the added value of each industry as the decision-making variable, and finally proposes the adjustment scheme with a relatively reasonable industrial structure variation and the largest emissions reduction. The manufacturing industries, as the main body of Ningbo's economic development, contributes a large part of pollutants and carbon dioxide emissions, and consume intensive energy and water resources. This paper explores the potential of Ningbo City to synergize the pollutants and carbon dioxide reduction through industrial structure adjustment under the three annual economic growth rates of 4.5%, 5.5%, and 6.5%. Results show that Ningbo City can achieve a maximum cumulative economic growth of 97% from 2020 to 2030 while achieving the goal of pollutants and carbon dioxide emissions reduction. On this basis, this paper puts forward suggestions for Ningbo City to facilitate industrial structure adjustment targeting the year 2030, including controlling the entry threshold for emission-intensive manufacturing industries, improving resource and energy productivity in the primary sector and mining industry, reducing pollutants and carbon dioxide emissions of electricity and heat production and supply industries further, and encouraging the development of high value-added tertiary industries and circular economy industry. The research can provide a decision-making reference for synergizing the reduction of pollutants and carbon dioxide emissions of the whole sector in Ningbo City and can also provide a valuable benchmark for promoting industrial structure optimization in other similar regions.