Digital infrastructure innovation in the new era is the important part of the digitalization of public health emergence governance, which means a complex evolution of the socio-technical system. In practice, the modular is identified as the effective approach in dealing with the complex innovation, which lacks of further study of the modular innovation of socio-technical system. In such context, according to the relative theory, this paper regards the information reporting and early warning system as the niche of infrastructural digitalization of public health emergence governance, and explore this digitalization process, explain how the technical niche and the organizational niche co-evolved in this process. Based on the case study, we found that China’s public health emergence governance information system has experienced three stages of modular co-evolution, namely exploitation modular innovation in the emergencies of the initial innovation, exploratory modular innovation in the normal context and integrating exploitation modular innovation in the emergencies of the evolving innovation. Specifically, during each stage, the selection of the co-evolutionary solution is based on the analysis of the socio-technical demand and supply, and then it optimizes the allocation of the socio-technical resources through technical modular and organizational modular. Also, it adjusts the complex environment by following the specific co-evolutionary solution according to the analysis of socio-technical demand and supply. Therefore, digital infrastructure innovation needs to combine the short-term and the long-term development in order to infiltrate the risk prevention and control into all aspects of infrastructure innovation. In the field of public health emergency and other professional areas, we should establish a forward-looking awareness, strengthen territorial authority, enhance social identity, and maximize the benefits of collaborative governance of technology and organization.