Abstract: Leveraging the overlapping advantages of multiple policies, including opening-up along the border and revitalizing border regions to benefit local populations, Agriculture in Yunnan Province has entered a critical transition period toward high-quality development. To clarify the interrelationships among the factors influencing agricultural development in Yunnan, their intertemporal transmission logic, and dynamic evolutionary characteristics, this paper used data from 16 prefectures and cities in Yunnan Province from 2016 to 2023 as the research sample and employed a dynamic Bayesian network model to identify the dynamic structure of the factors influencing high-quality agricultural development. The results indicated that: (1) The only key variables in Yunnan high-quality agricultural development system played a dominant role in intertemporal transmission. Among them, agricultural labor productivity, land productivity, the comprehensive mechanization rate of crop cultivation, planting, and harvesting, and the share of agricultural product market turnover were the most important dynamic drivers within the system. (2) There was a distinct state-dependent characteristics among the key variables, with changes in production efficiency and market connectivity states exhibiting strong dynamic association with subsequent states of resource utilization, ecological environment, and shared development. (3) The evolution of Yunnan high-quality agricultural development primarily manifested in three types of cross-dimensional transmission mechanisms: “technology-efficiency-green transition”, “market connectivity-resource optimization”, and “efficiency-ecology-welfare improvement”, indicating that high-quality agricultural development was not driven independently by a single dimension, but rather shaped by intertemporal interactions among four dimensions of technological efficiency, marketization level, resource-environmental performance, and livelihood-sharing. Accordingly, policy recommendations are proposed, including strengthening the foundational conditions for improving agricultural production efficiency, shifting green production from constraint-based governance to value conversion, and enhancing the organizational capacity of the specialty agricultural industry chain.