An in-vehicle complex biometric authentication system includes: a sensor to sense a driver's boarding of a vehicle; a controller to perform driver authentication based on biometric information sensed by multiple biometric sensors when driver's boarding in a vehicle is detected by the sensor, and to collect driver's identification information and driving habit information during operation of a vehicle when the driver authentication is succeeded; and a memory to store the identification information and driving habit information as implicit authentication information, wherein the controller further detects situation recognition information related to the implicit authentication information, after the driver authentication is succeeded, and determines whether to perform additional authentications based on the matching result of the detected situation recognition information with the implicit authentication information. According the present invention, the system can provide a biometric authentication system to which the IOT is applied.