Objective To study the epidemiological characteristics of special pathogenic infection in Wenchang area following the super typhoon "Yagi" disaster, and provide basis for the diagnosis, treatment, prevention and control of infectious diseases in disaster-affected areas. Methods Clinical characteristics and pathogenic data of 7 groups of patients infected with 9 species of zoonotic pathogens and opportunistic pathogens were analyzed retrospectively. The 7 groups included: pre-typhoon landfall group (August 6 to September 5, 2024), post-typhoon landfall group (September 6 to October 5, 2024), and groups in the past years of the same period (A2023, B2022, C2021, D2020, E2019, September 6 to October 5 of each year in 2019-2023). Epidemiological characteristics of patients as well as distribution and resistance of pathogens were compared and analyzed. Results In post-typhoon landfall group, 26 patients were infected. The overall infection rate of the post-typhoon landfall group was higher than all groups except B2022 group (all P<0.05). The infected cases mainly distributed in coastal areas. The main route of infection was outside the hospital (88.5%). Male accounted for 80.8%, agricultural workers accounted for 53.9%, and 69.2% of the cases occurred within 10 days after the typhoon. The major infection sites were multiple site co-infection, bloodstream infection, and soft tissue infection. The main pathogens maintained high sensitivity to commonly used antimicrobial agents. The accuracy of clinical initial empirical antimicrobial use was relatively low (45.5% in post-typhoon landfall group vs 62.8% in the groups of the same period in the past). The clinical cure rate decreased to 76.9%, and mortality increased to 7.7%. The mortality of patients infected with Burkholderia pseudomallei and kidney infected with Leptospira were 25.0% and 50.0%, respectively. Conclusion After typhoon disaster, special pathogen infection significantly increases and the prognosis is poor. It is recommended to emphasize blood culture and molecular biology testing to facilitate early diagnosis and precise treatment, optimize prevention and control measures, and enhance the accuracy of clinical empirical medication.