The complex adaptation system (CAS) theory of “adaptability to produce complexity” is a new theoretical perspective for the spatio-temporal evolution of rural tourism systems. Based on the CAS theory, the theoretical framework, structural composition, formation process, and evolution mechanism of the rural tourism complex system were examined and revealed. The suburban country region of Wuhan was taken as the area of focus for empirical research. The state of the rural tourism destination system in Wuhan has gone through various periods of development: the embryonic stage of the system (before 2000), formation (2001–2007), rapid development (2008–2015), and consolidation and transformation (since 2016). Under the environments stimulating external physical geography, social economy, market demand, and emergencies, multiple agents such as government, enterprises, residents, and tourists in Wuhan have actively adapted to the environment and other agents, and the interaction intensity and complexity have gradually increased, driving the emergence of system agent types, functional structures, and spatial patterns. The agents continue to grow, differentiate, and aggregate. The tourism product has shifted from the dominance of a rural ecological scenery and leisure agriculture to diversified development, and with the main function changing from sightseeing to leisure and vacation. The rural communities have been renovated and beautified, transforming them from a provider of rural service facilities to a co-builder of a rural-imaged tourism space.