Urban–rural integration is a top priority in social development and an urgent requirement for vigorously promoting rural revitalization. However, the current development of urban–rural integration in China still faces issues such as an unreasonable urban–rural industrial structure, unidirectional flow of rural population, and low sense of belonging among rural residents. Based on this, this paper selects eight cities from the Greater Bay Area as examples, organizing urban–rural integration development data from 1986 to 2022. It employs principal component analysis to quantitatively evaluate the evolutionary trend of urban–rural integration, constructs a fixed-effect panel quantile regression model to explore the factors influencing urban–rural integration and its spatiotemporal evolution, and uses threshold effects and interaction effects to test the threshold and application requirements for maximizing the benefits of urban–rural integration driving mechanisms, drawing empirical insights from comparisons with other bay areas around the world. The research found the following: First, between 1986 and 2022, the development of urban–rural integration in the Greater Bay Area steadily progressed, with gradually emerging effects, and industrial integration and population integration made significant contributions to the development of urban–rural integration. Second, the driving mechanisms of market economics, government intervention, and social fusion significantly impact urban–rural integration, with the influence of market economics being the most significant. Third, the impacts of the three driving mechanisms on urban–rural integration show temporal and spatial differences. In terms of time, market economics and government intervention always have a positive impact, while social fusion shows a “suppressing-promoting” trend, with a lower impact coefficient. Spatially, there are differences in strategies and priorities for promoting urban–rural integration in each region. Fourth, all three driving mechanisms exhibit threshold effects, and the explanatory power of any two interacting driving mechanisms for urban–rural integration development is stronger than that of any single mechanism. Notably, the combined interaction effect of the three driving mechanisms has the highest impact coefficient. The driving mechanisms should be implemented according to the principles of “synchronization, heterogeneity, and categorization”.