This study investigated the relationship between paternalistic leadership and intra-team conflict and the moderation effect of moral leadership within a university Crisis Management Team (CMT). Examined 312 paired samples from 33 CMT members and 800 of their subordinates at a public university in China, and our findings indicated that the CMT members showed a lower level of authoritarian leadership but a higher level of benevolent leadership and moral leadership during COVID-19. Benevolent and moral leadership were positively associated with cognitive conflict (β1 = 0.37, p < 0.01; β2 = 0.15, p < 0.05); meanwhile, authoritarian leadership was positively related to affective conflict (β = 0.17, p < 0.01). In addition, moral leadership significantly moderated the relationship between authoritarian leadership and affective conflict. Specifically, a higher level of moral leadership effectively suppresses the affective conflicts triggered by authoritarian leadership. This study provides a contextual explanation for the contradictions in the internal constructs of the theory of paternalistic leadership between the Eastern and Western points of view. In China, evidence found that moral leadership plays a core and coordinating role within the theory, which expands the literature in this field. At the same time, the conclusions of this study can provide a reference for educational institutions to cope with similar crisis situations in the future.