The invention provides an adjusting method of a system for changing a working frequency in an operation system for a computer system. The adjusting method includes establishing a look-up table, and detecting a newest value of the working frequency. An adjustment value can be obtained from the look-up table according to the newest value of the working frequency. In addition, a phase difference of a control signal of a memory is adjusted in the computer system according to the adjustment value and the working frequency is executed stably in optimum status according to the present invention.