Urban-rural integration is an important way to realize coordinated regional development, and the development of digital economy provides a new impetus for the improvement of urban-rural integration efficiency. This paper takes the urban-rural integration efficiency of Guangdong Province as the research object, and measures and analyzes the urban-rural integration efficiency of the region by using the decision-making model based on inputs and outputs (DEA-CCR) and the BCC model with variable returns to scale of production. The results found that the development level of digital economy is significantly and positively correlated with urban-rural integration efficiency, and there are differences in the integration efficiency driven by digital economy in different regions. The dynamic trend is further analyzed through the Malmquist index, and it is found that technological progress and efficiency improvement are the key factors affecting the integration efficiency. Accordingly, the following optimization strategies are proposed: strengthen the construction of rural digital infrastructure to enhance its digital access level; promote the deep integration of digital technology and rural industries to cultivate new business forms of rural digital economy; and promote the free flow and sharing of urban and rural data resources to enable the synergistic development of urban and rural industries.