Abstract: 【Objective/Meaning】The exploration on the development path of the rural governance system in the new era could meet the development demands of rural societies in the new era, and ensure the successful implementation of the rural revitalization strategy and the realization of the modernization goal of national governance.【Methods/Procedures】Based on the research perspective of good governance, and by taking the rural governance system of “three-governance integration” as the research object, the field investigation of Junying Village in Xiamen City was carried out by using the method of case study. Then, its practical condition and existing predicament were analyzed. Last, the corresponding practical paths were put forward.【Results/Conclusions】The research results showed that in the practice of rural governance, Junying Village has innovated the development model of “one core” led by the party building, improved the multiple autonomous organization system of the villagers, established a multiple-mediation dispute mechanism of “Yilitang”, cultivated the cultural roots and rural civilization. However, there were still some practical difficulties in the process of rural governance, such as the insufficient reserve of rural talents, insufficient motivation for the participation of the main body of villagers’self-governance, and inadequate construction of the rule of law in rural areas. Therefore, the path of constructing the rural governance system of “three-governance integration” was proposed from the four aspects of strengthening the construction of grass-roots party organizations, the construction of villagers’ autonomy, the rule of law construction in rural areas, and the rule of virtue construction in rural areas.