Based on the modernization goal of achieving common prosperity for all people, it is of great significance to explore the modernization transformation of urban-rural relationship. The modernization transformation of urban and rural relationship is the result of multiple factors, and its "integration and symbiosis" features promote the integration of urban and rural "economic-society", and build the urban-rural relationship with dual central significance. Through deconstructing the practice process of policy valuation, organizational empowerment and technological wisdom in urban and rural development, the modernization transformation of urban-rural relationship is manifested as urban-rural structural integration, balanced flow of elements and differentiated and complementary functions, and presents a reproduction process of value rationality, outcome rationality and instrumental rationality. Under the logic orientation of deficit order concept, dual-center development and digital dividend diffusion, the value of urban-rural relationship transformation has changed from differential order to deficit order, the effect view has changed from polarization development to cooperative production, and the method view has changed from efficiency to benefit sharing, which not only establishes a stable and orderly urban-rural relationship order, but also enriches the theoretical connotation of Chinese-style modernization. It also provides the wisdom to accelerate the common prosperity of all people.