Collaborative decision-making across multiple government agencies is considered a critical and effective strategy to combat public health crisis; however, we know little about how the collaborative decision-making works and evolves during periods of crisis. To fill this lacuna, this study uncovers the structure and evolving dynamics of the network by employing a policy document analysis. Based on the policy documents, jointly issued by the agencies of Chinese central government in four phases regarding COVID-19 control, we first constructed a co-occurrence matrix of policy-issuing agencies to outline the network structure, then drew a breadth–depth matrix to identify the role evolution of agencies, and lastly built a two-mode network consisting of policy topics and agencies to determine the evolution mechanisms of policy attentions for each agency. It was found that the network structure of interagency collaboration involves three forms: discrete structure in the early phase, subgroup structure in the middle phase, and connected structure in the latter phase. Agencies embedded in the network can be categorized into three types: leading agencies, key agencies, and auxiliary agencies, with their constituent members changed as the pandemic risks are gradually becoming under control. Furthermore, each type has its own primary policy attentions, but shares some common foci in all four phases and shifts attention in the emergency management process. This study contributes to shedding light on the formation of and variations in collaborative networks in health emergencies and provides policy implications for other countries that have struggled against COVID-19.