This study analysed the impact of the mechanism of the synergistic agglomeration of manufacturing and modern service industries on the high-quality development of the manufacturing industry using the entropy value method, coupling coordination degree, and E-G index. We utilised panel data of 30 provinces and cities in China from 2012 to 2022. The study found that synergistic agglomeration significantly promotes the high-quality development of the manufacturing industry, in which ‘new quality productive forces’ play a key intermediary effect, while the innovation ecosystem has direct and indirect moderating effects on the relationship between the two. Simultaneously, industrial synergistic agglomeration, development of new productivity, construction of innovation ecosystems, and high-quality development of the manufacturing industry in all provinces and cities showed a steady increase; however, there were significant differences between regions. Based on the findings of the study, policy recommendations are suggested to further promote the synergistic development of the manufacturing industry and modern service industry. At the policy level, the government should strengthen the guidance and support of industrial synergistic agglomeration and formulate differentiated policies to promote industrial synergistic agglomeration; simultaneously, it should pay attention to the cultivation of new productivity and the construction of innovation ecosystems, optimise the allocation of innovation resources, and stimulate the vitality of innovation. At the industrial level, manufacturing enterprises should actively cooperate with modern service enterprises to achieve resource sharing and technological complementation; modern service industries should improve service quality and efficiency to meet the needs of manufacturing transformation and upgrading; and close cooperation between the industry, academia, and research institutes should be established to promote technological innovation and industrial upgradation.