Emergency science communication is an important emergency activity that can enhance public safety awareness and risk perception ability, optimize health-protective behaviors, and reduce losses from emergencies. Certainly, emergency science communication needs to be multisource information and cross-organization. Moreover, increasing cooperation in emergency science communication is the key to improving the effectiveness of science communication in public health emergencies. To clarify the cooperation relationships among emergency organizations in emergency science communication, emergency science communication cooperation networks (ESCCNs) are constructed on the basis of the social network analysis method, and the practice of emergency science communication in response to COVID-19 in China is taken as the case. Through an interpretation of the characteristics of ESCCNs in the emergency response phase and the ongoing emergency phase, the differences in the cooperation modes of public health emergencies in different phases are analyzed. Moreover, the influence of different emergency phases on the formation of the ESCCN of the whole phase is discussed. With the evolution of the emergency phase, the network tightness, equilibrium and connectivity of the ESCCN all tend to increase, whereas network agglomeration decreases. In the emergency response phase, the core-edge features of the ESCCN are obvious, and emergency science communication organizations (ESCOs) are more inclined to form emergency science communication cooperation with other ESCOs of the same type. However, in the ongoing emergency phase, the cooperation relationships between ESCOs are more balanced, and more diversified cross-group cooperation relationships are formed. The diversification of ESCO types, the closeness of ESCO relationships and the connectivity of ESCCNs are the main factors that promote the formation of the ESCCN of the whole phase. Furthermore, implications for strengthening the efficiency of science popularization cooperation in public health emergencies are proposed in connection to matching dynamic characteristics, optimizing resource allocation and strengthening institutional guarantees.