In the context of Disease X risks, how governments and public health authorities make policy choices in response to potential epidemics has become a topic of increasing concern. The tightness of epidemic prevention policies is related to the effectiveness of the implementation of measures, while the organizational cognition of epidemic risks is related to the rationality of policy choices. During the three years of COVID-19, the Chinese government constantly adjusted the tightness of its prevention policies as awareness of the epidemic risk improved. Therefore, based on the epidemic risk organizational cognition model, the key nodes that affect the tightness of epidemic prevention policies can be explored to find the organizational behavior rules behind the selection of prevention policies. Firstly, through observing the adjustments made to the Chinese government’s prevention strategies during the epidemic, a time-series cross-case comparative analysis reveals how policy tightness shifted from stringent to lenient. This shift coincided with the organizational cognition of epidemic risk evolving from vague to clear. Secondly, by building the “knowledge-cognition” coordinate system to draw the organizational cognition spiral of epidemic risk, it is clear that the changes in the tightness of the prevention policies mainly came from the internalization and externalization of knowledge such as epidemic risk characteristics to promote the level of organizational cognition, which is manifested as expansion and deepening. Thirdly, the node changes in the interaction between organizational cognition development and policy choice proved that different stages of the epidemic had diverse environmental parameters. Moreover, as the epidemic nears its end, the focus of policy tightness is shifting from policy objectives to policy implementation around governance tools. The results indicate that organizational cognition of epidemic risk exhibits significant stages and periodicity. Additionally, epidemic risk characteristics, environmental coupling, and governance tools are crucial factors in determining the tightness of epidemic prevention policies.