The construction of the "three-in-one" rural governance system is not only the basis and premise of promoting the modernization of the national governance system and governance capacity，but also the proper connotation of realizing the modernization of the rural governance system and governance capacity.It provides an effective methodology for the promotion of Rural Vitalization.in practice，the construction of the "three-in-one"rural governance system is faced with multiple practical challenges，such as the weakening of its autonomous function，the obvious decline of the original traditional value system in the countryside，and the dilemma between affinity and law in rural construction.A series of measures should be taken，such as strengthening the leading ability of rural grassroot party organizations for the "three-in-one governance"，improving the villagers''self-governance system and supervision system，establishing and improving the moral education system and the legal guarantee system，etc，to truly realize the guiding function of party building.The organic integration of self-governance，rule of law，and rule of virtue under the rule of law activates the endogenous order of rural societythrough institutional supply and improve the modernization and socialization level of rural social governance，so as to achieve the purpose of strengthening institutional supply，and ultimately realize the effective governance of rural society.