Abstract: The present invention provides a method of downloading a configuration code, applied in a timer/counter control register, and the method comprises steps of acquiring a first boot code through a first default interface of the timer/counter control register; calculating a first check code according to the acquired first boot code; determining whether the calculated first check code and a first standard check code are the same; as the two are the same, downloading the configuration code from the storage element coupled to the first default interface through the first default interface; as the two are different, downloading the configuration code from a storage element coupled to a second default interface through the second default interface of the timer/counter control register. Therefore, the present invention promote the utility flexibility of the timer/counter control register. The present invention further provides a system of downloading a configuration code and a timer/counter control register.