The invention relates to a USB (universal serial bus) identity authentication method based on voiceprint recognition and a system thereof, belonging to the technical field of computer information safety. The system comprises a user terminal and an embedded voiceprint recognition hardware system based on USB, wherein the user terminal and the embedded voiceprint recognition hardware system based on USB are connected by a USB bus; the embedded voiceprint recognition hardware system based on USB comprises a central processing unit for finishing authenticated voiceprint recognition operation, and the central processing unit is respectively connected with a voice acquisition unit, a data storage unit, a power supply management module, a state indication module and a USB interface used for connecting the user terminal. The invention has the advantage of higher safety. The invention also can provide third-party application and service voiceprint certification interface, and can expand to fields, such as internet banks, e-commerce, e-government affairs and the like.