Objective To analyze epidemiological characteristics of the first case of avian influenza virus(H5N6) infection in human in Anhui province. Moreover, to review the case detection, survey and treatment. Furthermore, to provide reference for survey and treatment of avian influenza virus(H5N6) infection in human. Methods According to The Master State Plan for Rapid Response to Emergencies of Highly Pathogenic Avian Influenza Infection in Human and The Anhui Province Technical Protocols for Rapid Response to Emergencies of Avian Influenza Infection in Human, we carried out epidemiological study and treatment, including the history of exposure to poultry, the process of diagnosis and treatment, close contacts, local incidence of influenza-like illness, specimen( patient, close contacts and surroundings which patient may be exposed to poultry) collection and detection. Results In Anhui province, the first case infected with H5N6 influenza virus had a clear history of exposure to sick or dead poultry. There was no secondary cases occurred in close contacts. The H5N6 subtype influenza virus detected in some surrounding samples. Conclusion The first case of avian influenza virus(H5N6) infection in human was local infection in Anhui province. The possible route of infection was contact with sick or dead poultry. To improve medical diagnostic sensitivity and to strengthen the monitoring of pneumonia of unknown causes is an important means of timely detection and treatment for epidemic of human infected with avian influenza A(H5N6) virus. The live poultry markets closed for disinfection is a key measure to control the epidemic.