The present invention discloses a method, related to smart card reader field, for recognizing a card reader with multiple card holders. The method includes connecting, by the card reader with multiple card readers, to a host and loading, by the host, card reader device bus driver; obtaining, by the card reader device bus driver, the device information of the card reader with multiple card readers and creating physical device object according to the device information; installing and loading, by the host, smart card function driver for each physical device object and registering a standard smart card driver library for every smart card function driver; creating, by the smart card service of the host, a new smart card device record in the resource manager of the smart card service according to the smart card function driver loaded and the smart card driver library registered and recognizing the card reader with multiple card readers as a plurality of smart card devices. The invention further discloses a method for communicating between the host and the card reader with multiple card holders based on the recognizing method described above and a system thereof.