The internet age and the rapid development of network information technology have built cyberspace. As a social public space with the most contemporary significance, cyberspace has bred a new way of human virtual existence and the form of social existence of virtual society. Cyberspace and the space turn have expanded the ideological and political education horizon. The study of ideological and political education in cyberspace is a new field full of temptation and vitality. Cyberspace provides a new practical environment for ideological and political education governance in colleges and universities. The ideological and political education governance of colleges and universities in cyberspace is an important part of the modernization of state governance system and governance capacity. At present, the ideological and political education governance of colleges and universities in cyberspace is faced with many challenges, such as the multiple pressures of cyberspace ideology, the dilemma of extension of traditional ideological and political education to cyberspace, and the anomie of college students' thoughts and behaviors. The ideological and political education in colleges and universities must adapt to the requirements of the development of internet, strengthen the consciousness of the problems of cyberspace, carry out the fundamental task of setting high moral values and cultivating person, and maintain the ideological security of colleges and universities. It is very important to put forward a more explanatory, influential and persuasive network ideological and political education governance composition from the new level of cyberspace to seek solutions. Based on Marxism system thought and human subjectivity ideology, the innovation and development of ideological and political education governance in colleges and universities based on cyberspace is embodied in four aspects:system reconstruction and collaborative construction, information production and supply and demand balance, order regulation and vitality creation, dynamic opening and value dialogue, so as to achieve the innovation of ideological and political education governance ideas, methods, paths and mechanism. Among them, idea innovation is the fundamental, method innovation is the key, path innovation is the foundation, mechanism innovation is the guarantee.