As an important engine for high-quality economic development, the digital economy is gradually integrating with the rural logistics industry. This trend is contributing to making rural logistics a fundamental, strategic, and pioneering industry. However, some valuable topics remain unstudied, such as whether they are coupled and whether there is variability in the coupling system across the provinces. Therefore, this article takes system theory and coupling theory as the analytical framework, aiming to better elaborate the subject’s logical relationship and operational structure of the coupled system, which is composed of a digital economy subsystem and a rural logistics subsystem. Furthermore, 21 provinces are seen as the research object in China, and the coupling coordination model is constructed, aiming to verify the coupling and coordination relationship between the two subsystems. The results suggest that two subsystems are coupled and coordinated in the same direction, and they feed back and influence each other. During the same period, four echelons are divided and there is variability in the coupling and coordination between the digital economy and rural logistics, according to the coupling degree (CD) and coupling coordination degree (CCD). Findings presented can serve as a useful reference for the evolutionary laws of the coupled system. The findings presented here can serve as a useful reference for the evolutionary laws of coupled systems. Moreover, it further provides ideas for the development between rural logistics and the digital economy.