Colleges and universities are the educational institutions that aim for the cultivation of the high-quality talents, so they are highly concerned by the public. In the current times of new media information dissemination, great changes have taken place in the content and mode of information dissemination, especially in the pluralism of the subject and form of information dissemination, which makes it necessary for higher education institutions to conduct scientific guidance of public opinion. Only in this way can we guarantee the correct communication image of colleges and universities. But from the current actual situation, the negative news of a large number of colleges and universities make a lot of colleges and universities receive different evaluations of the public image, and the bad evaluations constrain the development of these schools. In this paper, the author carries on the detailed research on the public opinion guidance of the higher education institutions in the times of new media information dissemination. Public opinion has the characteristics of persistence, intensity and consistency, and it plays an important role in social development and social stability. There are lots of students and staff in colleges and universities, and as the educational institutions for cultivating higher-quality talents; they are highly concerned by the public, even they are the institutions that can easily cause the attention of the public opinion. In the times of new media information dissemination, compared with the traditional elements, the speed, form and subject of the current information dissemination have greatly changed, and the public opinion communication in colleges and universities has these characteristics - diversification of subject, complexity in content, diversification of influence. In recent years, there have been a lot of negative public opinion events in colleges and universities, which have brought about a bad impression on the positive image and future development of colleges and universities. How to guide public opinion correctly of the higher education institutions has become an important issue in the development of colleges and universities. In this paper, the author sums up a large number of studies and cases, discusses the challenges in the guidance of public opinion in colleges and universities in the times of new media information dissemination, and puts forward some countermeasures.