An iris identification system for confirming identity of a person and method thereof are disclosed. The iris identification system comprises a mode converter for selecting one of registration and identification modes, an image input means, a luminance adjustment module, a registration module, an identification module, a reference iris image storage, and a main control unit. The registration module captures iris images when the registration mode is selected, preprocesses the captured iris image, defines the preprocessed iris image as main, auxiliary, negative main and compensation data, encodes the defined data, and registers the encoded data as data of the reference iris images; The identification module captures an iris image when the identification mode is selected, preprocesses the captured iris image, defines the preprocessed iris image as main, auxiliary, negative main and compensation data, encodes the defined data, and analyzes similarity both data.