Objective This study synthesizes field-based practices in public health emergency response during the 2025 summer flooding in Beijing, identifies prevailing gaps in current operations, and proposes targeted recommendations to inform and strengthen flood-related health emergency governance systems in megacities.

Methods Using retrospective analysis and focus group methods, the study summarizes the organization, implementation, material support, technical measures, and management mechanisms of Beijing′s 2025 summer flood disaster health and epidemic prevention work.

Results Through high-level overall planning, inter-departmental collaboration, targeted policy formulation, grassroots implementation and public engagement, Beijing has steadily advanced post-disaster health and epidemic prevention work in an orderly manner and realized the objective of "preventing major epidemics in the aftermath of disasters". Nevertheless, several challenges remain: imperfect cross-departmental coordination mechanisms, emergency plans lacking sufficient pertinence and operability, inadequate grassroots capacity and supporting resources for epidemic prevention, imprecise health education delivery, as well as disjointed efforts between health supervision and technical epidemic prevention work.

Conclusion Beijing′s overall response to the summer flood epidemic emergency was timely, with relatively systematic measures and strong execution. In the future, efforts should be made to further improve cross-departmental coordination mechanisms, refine plans and standardized procedures, strengthen grassroots epidemic prevention teams and funding assurance, enhance the accuracy of health education, clarify the boundaries between supervision and law enforcement and technical epidemic prevention responsibilities, and continuously improve the emergency management capabilities of epidemic prevention in capital city flood disasters.