An operating method and system of a customized interface system are provided. The method includes setting, by a controller, a plurality of manipulation regions in a customized input interface and mapping a first manipulation region among the plurality of manipulation regions to a first function among a plurality of functions provided from an information technology (IT) device. In addition, the controller is configured to recognize a user's finger based on an image photographed by an imaging device and execute the first function when a position of the user's finger corresponds to the first manipulation region.