In recent years, China has achieved significant breakthroughs in both the quantity and quality of agricultural scientific and technological innovations. Advancing the transformation of scientific and technological achievements in rural areas has become a pivotal pathway to promote urban-rural integration development and achieve common prosperity. However, the persistent disconnection between agricultural scientific innovation and economic development, often referred to as the “two-layer problem”, remains a significant challenge. This issue urgently necessitates the construction of efficient transformation mechanisms to bridge the “last mile” gap in the practical application of scientific achievements. Taking China’s National Urban-Rural Integration Development Experimental Zones as a focal point, this study systematically analyzes the central government’s top-level policy designs and local exploration practices. The findings reveal that these pilot zones have initially established effective models for leveraging technology to support urban-rural integration through measures such as promoting the downward flow of scientific and technological talent into rural areas, fostering collaborative mechanisms among government, industry, academia, research institutions, and end-users (the “government-industry-university-research-application” synergy), building technology service platforms, and improving full-chain transformation systems. Nevertheless, deep-seated issues persist, including insufficient innovation momentum among key actors, barriers to the mobility of urban and rural factors, and inefficiencies along the transformation chain. To address these bottlenecks, this study, drawing on pilot zone experiences, proposes three optimization pathways: 1) reconstructing a demand-driven research ecosystem to stimulate collaborative innovation vitality among diverse stakeholders; 2) establishing sustainable mechanisms for the long-term retention of rural talent through institutional empowerment and incentive alignment; and 3) improving comprehensive service systems for full-chain transformation to break through bottlenecks in technology diffusion and application. This research aims to provide institutional references and practical support for enhancing the efficiency of scientific and technological achievement transformation in rural areas, thereby promoting high-quality urban-rural integration development.