A configuration setting circuit and the method thereof, in which the configuration setting circuit includes a clock generator, a plurality of terminals, and a frequency detector coupled to a terminal. The clock generator is used to generate multiple clock signals with different frequencies, and output through the terminals. One input signal is inputted to the frequency detector through the terminal coupled to the frequency detector, so that the frequency detector can output at least two-bit configuration signal corresponding to the frequency of the input signal to set the operation mode.