The paper holds that under the background of comprehensively advancing the rule of law, the university governance by law is faced with the following four practical obstacles and main problems: (1) the weak awareness of the rule of law and the lack of authority of laws and regulations; (2)the imperfect educational laws and regulations and the imperfect rules and regulations system; (3) the weak enforcement of the rules and regulations and the existence of the phenomenon of non-compliance of the law; (4) a lack of legal due process guarantee and right relief mechanism for running schools according to law. This paper makes a comprehensive, systematic and specific in-depth analysis on the above four aspects of their respective basic connotation, specific performance and causes so as to provide theoretical and factual basis for promoting colleges and universities to take targeted measures and achieve obvious results.