With the refinement of division of labor, manufacturing enterprises are gradually outsourcing non-core processes. This trend not only promotes the specialized development of productive service industries, but also brings opportunities for the upgrading of the manufacturing industry. In the context of the digital economy, digital technology has gradually become a key driving force for industrial integration and development. Based on this, under the conditions of the digital economy, the integrated development mechanism of productive service industry and manufacturing industry was taken as the research object, and a logistic evolution model was constructed to empirically study the integrated development dynamics of various comprehensive economic zones in China from 2019 to 2023. Research has found that the integration of productive services and manufacturing industries in various comprehensive economic zones presents regional differentiated development characteristics. The evolution coefficient of each comprehensive economic zone shows an increasing trend, indicating that the overall development of the integration of the two industries is improving. However, there are significant regional differences, manifested in three typical patterns: fluctuation type (Northeast and Southwest Economic Zones), convergence type (Southern Coastal and Northern Coastal Economic Zones), and convergence type (Eastern Coastal and Yellow River Midstream Economic Zones). Under the conditions of the digital economy, the evolution effect coefficients of various comprehensive economic zones exhibit three scenarios: identical trends, decreasing differences, and fluctuating trends. However, regional differences are significant, showing heterogeneous effects (promoting or inhibiting effects). That is, except for the southern coastal comprehensive economic zone, the digital economy has had varying degrees of hindering effects on the integrated development of the two industries in other comprehensive economic zones. By strengthening digital technology infrastructure and standardization, improving the data governance system, cultivating compound talents, and building an integrated ecosystem, the inhibitory effect of the digital economy on the integration of the two industries can be effectively alleviated, promoting the formation of a high-quality development pattern of "promoting integration with data and promoting innovation through integration". It provides an important basis for formulating differentiated regional digital economy development policies.