Yu Zisan, a member of the CCP’s affiliated organization, was arrested and then tortured to death in 1947. After his death, the KMT authority of Zhejiang province not only delayed announcing the news, but also fabricated conversation transcripts and circumstances of death. Meanwhile, through the students’ union of Zhejiang University, the CCP had been developing a student movement that boycotted classes. However, as the processes of the student movement began, the CCP’s estimation of the initial situation was overly optimistic, and subsequently, it moderated the movement’s strategy. Zhu Kezhen, as Zhejiang University’s Chancellor, thought that university students should have the freedom of belief, but not of political activity. Zhu approved solving the Yu incident through legal channels, but faced a dilemma in reality as result of the confrontational KMT-CCP situation. Although Chiang Kai-shek demanded the Zhejiang authorities strictly punish students, he was reluctant to express his opinion openly. Zhang Chun asked Zhejiang authorities to make the truth known to the public. Thus, Zhejiang authorities were initial extremely careful, opening details of the Yu incident in order to change public ideas, adjudging other students in public, and announcing temporary martial law to suppress the student movement. The Ministry of Education mediated the difference of opinions between Zhejiang University and the local authorities. With the student movement continuing, regardless of the Zhejiang authorities or the Ministry of Education decision to suppress it, ultimately the beating death occurred. After the Yu Zisan student movement, these Zhejiang University students became more radical. This case study can clarify the historical facts, and also show the dilemma that universities faced in the period of civil war.