A zoonoses prevention system and prevention method thereof is disclosed. By storing an animal vaccination record into a near field communication (NFC) chip of an animal end, and storing an user vaccination record into a portable device with NFC, and receiving the animal vaccination record as well as transmitting the animal vaccination record and the user vaccination record to a server through the internet when the portable device scans the NFC chip, so as to generate a recommendation report according to a comparative analysis of the user and animal vaccination record by the server, and transmitting the recommendation report to the portable device for outputting. The mechanism is help to improve the convenience of zoonoses prevention.一種人畜共通傳染病的預防系統及其預防方法,透過在寵物端的近場晶片儲存寵物疫苗施打紀錄,以及在具近場通訊(Near Field Communication, NFC)功能的可攜式裝置儲存使用者疫苗施打紀錄,當具NFC功能的可攜式裝置感應寵物端的近場晶片時,接收寵物疫苗施打紀錄並與使用者疫苗施打紀錄一併透過網路傳送至伺服端,由所述伺服器根據疫苗施打紀錄比對分析產生建議報告,並且將此建議報告傳送至可攜式裝置以進行輸出,用以達成提高預防人畜共通傳染病的便利性之技術功效。110‧‧‧寵物端120‧‧‧伺服端130‧‧‧可攜式裝置131‧‧‧儲存模組132‧‧‧感應模組133‧‧‧傳輸模組134‧‧‧輸出模組