The fundamental task of the modernization of rural governance system is to construct and perfect the rural governance system and implementation mechanism. As an important component of the rural governance system，China’s rural deliberative system has gone through three important stages of institutional change： system replacement， system gradual transformation and system adaptive regeneration in the past hundred years. With the change of the subject relationship，there have been at least five different system forms， namely， traditional elite-dominated consultation， democratic mobilization consultation， communal centralized consultation， villager autonomy consultation and multiparty governance consultation. Although the rise of Western consultative democracy theory has led to a shift in the domestic discourse，the change of China’s rural deliberative system has its intrinsic trajectory .The state and farmers constitute agents of the rural deliberative system change. The relationship between farmers and land affects the order foundation of the rural deliberative system change. System ambiguity and system friction are structural motives of the institution change . Furthermore，combined with the strategy of rural vitalization，the rural deliberative system can be improved from systematization of system construction，the adaptability of system practice，the clear boundary of system function and the flexibility of system innovation，etc.