At present, the frequent public opinion events caused by the public relations crisis of colleges and universities on the Internet reflect the disharmony between the internal and external communication environment of colleges and universities. Faced with various challenges brought by new media, colleges and universities need to actively reform the organizational structure, change the organizational communication mode, and improve the efficiency of organizational communication. This paper tries to summarize the challenges in the context of new media from the public relations crisis in colleges and universities, and gives some countermeasures from the perspective of organizational communication.