Rural industrial integration refers to the process of relying on technological innovation and industrial model innovation to promote the optimal allocation of factors such as land, capital, and labor in rural areas, promote the optimization of a rural industrial structure, rural property rights stability, agricultural and rural development, and ultimately achieve the extension of the agricultural industry chain and improvements in farmers’ income levels. In order to grasp the mechanism of digital economy and rural land certification on rural industrial integration, this paper analyzes the impact of digital economy development and rural land certification on rural industrial integration based on the 2011–2021 panel data of the Yangtze River Economic Belt at the municipal level. Research has shown the following. (1) The early development of the digital economy significantly promoted the integration of rural industries. After overcoming the turning point of the digital economy, the digital economy has a restraining effect on the integration of rural industries; in terms of controlling variables, the education level of rural residents, regional economic development level, per capita disposable income of rural residents, and rural power generation all significantly promote the process of rural industrial integration. (2) Rural land certification has played a positive transmission role by confirming, reviewing, and registering land ownership in accordance with the law, clarifying the ownership of land rights, providing a stable property rights foundation for rural industrial integration, and effectively promoting rural industrial integration. (3) The impact of the digital economy on rural industrial integration has a single threshold effect, and after crossing the threshold value of a rural population, the positive impact of the digital economy on industrial integration is more significant. (4) The development of the digital economy has significantly improved the integration level of rural industries in this region and neighboring areas. The above conclusions have important policy implications for further leveraging the digital economy to promote the integration of rural industries and the modernization of agriculture and rural areas.