Emergency management, a vital administrative activity involving multiple parties collaborating to respond to sudden incidents to ensure urban safety, is hindered by the barriers in information and resource sharing among government sectors. Enhancing the collaboration level among government sectors is a significant research issue in the digital transformation of urban emergency management. To accurately grasp the derivative logic and development path of government emergency management sector collaboration in digital transformation, this paper carries out a case study of S City, a megacity in China. The study analyses key theoretical components such as goal, initial conditions and driving forces, structure, and processes, and constructs a theoretical model of digital collaboration in emergency management. The study finds that: (1) Under the dual drive of internal and external forces, the initial “hardware and software” directly affects the initial effects and development speed of digital collaboration. (2) The interaction of three elements—data, institution, and technology—can reduce the complexity and rigidity of the collaborative structure and promote diversity in collaboration modes. (3) A sustainable emergency management digital collaboration system depends on three crucial features: flexibility of mechanisms, robustness of structures, and dynamic adaptability of processes. At the practical level, this paper, in conjunction with S City’s explorations, extracts three key combination of strategies (empowerment + service, accountability + consensus, compliance + autonomy) to drive the digital collaboration process in emergency management. The above research results deepen the theoretical understanding of digital transformation in emergency management and cross-sector collaboration, and also provide insightful references for other provinces and cities in China to break digital barriers and achieve digital collaboration in emergency management.