Abstract: Rural space is an important field and the starting point for the realization of rural revitalization and the modernization of national governance. The rural spatial governance under the influence of the urban value logic in the past cannot meet the needs of the new stage of rural development, and it is urgent to carry out targeted research on rural spatial governance from the perspective of rural ontology. Based on the analysis of the realistic predicament of rural spatial governance and the historical evolution of urban-rural relations in China, the theoretical connotation of the rural subjectivity perspective and the value logic of rural spatial governance under the background of rural revitalization are reconstructed and the targeted practical path is explored. The following findings are obtained. First, the key point of rural spatial governance is pursuing a sustainable urban-rural relation and seeking the dominant position of the rural in the new era. Second, the rural subjectivity is the initiative of the rural when facing the demands of transformation and development. Its theoretical significance emphasizes the endogenous growth consciousness, highlights the rural cultural individuality and the diversity of inclusive development paths. From the perspective of rural subjectivity, the value logic of rural spatial governance turns to multi value, villager subject and life leading. Third, based on the perspective of rural subjectivity, the implementation path of rural spatial governance can be launched from four aspects: improving the living environment, promoting the village industrial economy, improving the county social governance and optimizing the urban-rural spatial pattern.