The construction of the modern rural governance system becomes an important part in promoting the urban-rural integration development and rural vitalization. Solving systemic problems such as limited development space, unclear ownership relationship and inefficient organization in the process of using rural space has become the primary task of rural spatial governance. Based on the breakthrough of the comprehensive governance of "matter-ownership-organization" in rural space, this paper attempts to analyze the mechanism of rural space governance in promoting rural space restructuring, ownership reshaping and organizational system reconstruction, and further explores the feasible path of rural space governance to optimize the urban-rural pattern, improve the urban-rural interaction, and promote the urban-rural integration development. The conclusions are as follows: (1) Physical space governance facilitates the optimization of rural spatial structure, the space ownership governance safeguards the development rights of different stakeholders, and the space organization governance enhances rural organizational capabilities. The comprehensive governance of "matter-ownership-organization" in rural space helps to impel the restructuring of rural space, the reshaping of ownership relations and the reconstructing of organizational system, to achieve the goals of the modern rural space governance system with clear rural space ownership. (2) The "population-land-industry" transformation path guided by rural space governance creates conditions for the analysis of "deepening space governance-activating rural space-optimizing human-land relationship-improving the urban-rural pattern". (3) Rural space governance promotes the continuous evolution of urban-rural development, and the improvement of urban-rural interaction becomes an important basis for upgrading urban-rural integration development and solving the dilemma of rural development. Finally, this paper constructs an analytical framework and feasible path for the interaction between rural space governance and the urban-rural integration development, and explores the internal relationship and research trends of rural space governance and territory spatial planning.