An electronic apparatus and a secure boot method thereof are provided. The electronic apparatus includes at least two connecting devices and a storage device. In the method, a current configuration of the connecting devices is detected, in which the current configuration includes one or a combination of a number, types, specifications and identifications of external devices connected with the connecting devices. Then, multiple preset configurations recorded in the storage device are retrieved and compared with the detected current configuration. If the current configuration matches one of the preset configurations, an apparatus function corresponding to the matched preset configuration is executed.