The invention discloses a prevention system of zoonosis and a prevention method thereof. The method comprises the steps of storing a pet vaccinating record on a near field chip of a pet end and storing a user vaccinating record on a portable device with a Near Field Communication function, receiving the pet vaccinating record and transmitting the pet vaccinating record together with the user vaccinating record to a server side through the network when the portable device with the Near Field Communication function senses the near field chip of the pet end, making the server side conduct comparative analysis and generate a suggestion report according to the vaccinating records, and then transmitting the suggestion report to the portable device to be outputted. In this way, the technical effect of improving the convenience in preventing zoonosis is achieved.