In recent years, food safety accidents have occurred frequently in colleges and universities, and students are prone to emotional resonance with food safety. It triggered heated discussions among the whole society and gradually formed a unique online public opinion on food safety in universities. After food safety incidents broke out in universities, some universities deliberately avoided responsibility or made mistakes in handling the incidents, which will create greater risks of online public opinion. Therefore, this paper takes the “Rat Head and Duck Neck” incident at Jiangxi Institute of Technology in China as an example. The purpose is to study the dissemination of public opinion on food safety online in universities and propose emergency countermeasures. Above all, the food safety online public opinion is divided into five stages: incubation period, burst period, spreading period, recurring period and dissipation period. Then, methods such as text mining and cluster analysis were used to deeply analyze the influencing factors at each stage of the development of food safety online public opinion. And analyze the role of different subjects in the development of public opinion based on the perspective of stakeholders. Finally, this paper provides corresponding countermeasures for different stages of online public opinion on food safety in universities, which provides suggestions and references for university governance. This study found that: (1) The resonance effect of online public opinion media on food safety in universities is significant. (2) Public opinion on food safety in universities is repetitive. (3) Improper response to food safety incidents in universities can easily trigger negative secondary public opinion.