Abstract: The construction of rural governance system has become an important part of promoting the construction of national governance system in the new era. At present, the construction of rural governance system in China is faced with the challenges of the leadership of grass-roots party organizations to be strengthened, the disorder of grass-roots democratic autonomy, the risk of involution of grass-roots rule of law, the weakening of the binding force of moral norms, and the lack of the ability to deal with contradictions and disputes. Based on the new era, the thesis puts forward a new system of rural governance modernization of "five governance coordination", which covers the following aspects: politics as the core of leadership, autonomy as the foundation, rule of law as the guarantee, moral rule as the guidance and intellectual governance as support.