Abstract: In order to analyze the main contradiction of the Sannong issues (agriculture, rural community and farmers) at the micro level and propose countermeasures systematically, through on-the-spot investigation and organizing seminars, present situation and focuses of the Sannong issues in Yazhou District were investigated, and basic economic data of Yazhou District were collected and analyzed. The results showed that the Sannong issues were a contradictory set of disadvantaged agriculture, weak farmers and poor rural communities. The contradictory set was produced by the combined effects of the natural and social conditions. The issues were the complexity and variety of agricultural system, the lack of an overall coordination of government actions, the bottlenecks of rural economic and social management, the difficult problems of farmers, the imperfection of rural finance, the weakness of infrastructure and public services, and so on. Through improving the harmonious structure of the rural governance by the “three dimensions in one”, the micro system operational mechanism of the Sannong issues was proposed. Besides, the author recommended that the local party committees and governments should make full use of the role of national policy, reform micro level of Sannong issues deeply, optimize and integrate the resources, introduced a range of approaches and measures according to the problems, improve the hard and soft environments inside and outside, mobilize the enthusiasm of all parties to resolve specific conflicts of the Sannong issues, and help to increase farmers’ income, improve agricultural efficiency and develop the rural communities.