This study seeks to improve urban supply chain management and collaborative governance in the context of public health emergencies (PHEs) by integrating fuzzy theory with the Back Propagation Neural Network (BPNN) algorithm. By combining these two approaches, an early warning mechanism for supply chain risks during PHEs is developed. The study employs Matlab software to simulate supply chain risks, incorporating fuzzy inference techniques with the adaptive data modeling capabilities of neural networks for both training and testing. The results demonstrate that the proposed model effectively identifies factors contributing to supply chain deterioration, with a warning error as low as 0.001, significantly enhancing the accuracy and timeliness of demand forecasting. The BPNN algorithm, through its self-learning and adaptive features, facilitates dynamic optimization and precise scheduling across various stages of the supply chain. This capability is particularly valuable in addressing challenges associated with sudden demand spikes and resource allocation. As a result, the mechanism is able to accurately and promptly identify adverse trends in the supply chain, thereby enhancing the efficiency and flexibility of urban emergency responses, mitigating risks, and offering both theoretical and practical contributions to urban collaborative governance.