A clock frequency adjusting system is disclosed. The clock frequency adjusting system includes a sensing clock generating unit, a frequency-dividing unit and a controller. The frequency-dividing unit makes frequency of the sensing clock signal be divided by a frequency-dividing modulus and then outputs a clock calibration signal. The controller includes a period counter and a frequency adjusting unit. The period counter samples the clock calibration signal through the external clock signal so as to acquire a second count value. The frequency adjusting unit calculates a frequency difference data between the clock calibration signal and the predetermined clock signal according to the first count value and the second count value, and determines a number of adjustment according to the frequency difference data and a step adjusting frequency so as to output a clock adjusting signal to the sensing clock unit to adjust frequency of the sensing clock signal.