Big data has become an important tool to promote the transformation of higher education governance. Big data enables higher education governance to transform its governance structure, expand its governance subjects, expand its governance boundaries and innovate its governance rules internally. In terms of value logic, big data enables higher education governance to be mainly embodied in shaping data thinking, reconstructing value cognition, surpassing technical rationality and realizing characteristic development. At present, the governance of higher education enabled by big data has some practical dilemmas, such as lack of system guarantee for data application, weak research ability of data technology, information risk of databased governance and weak humanistic care of technologybased governance. In the future, it is necessary to further standardize data governance, and improve the modern university system with Chinese characteristics; explore the value of the data, and stimulate the internal power of higher education governance; be based on the overall data, and achieve collaborative governance of higher education; interpret the data in depth, and highlight the peopleoriented value orientation.