A frequency adjusting method of a CDR circuit and apparatus thereof are provided. The adjusting method is applied to a receiver apparatus connected to an outer apparatus. The outer apparatus, after actuated, sends out an outer data signal to the receiver apparatus according to its operational frequency and a PLL of the receiver apparatus outputs a transmitter clock according to an operational frequency of the receiver apparatus. The CDR circuit of the receiver apparatus generates a receiver clock according to the outer data signal. The CDR circuit is set in a phase mode such that the receiver clock follows transmitting frequency of the outer data signal. Then, a difference between frequencies of the receiver clock and the transmitter clock is checked. If the difference is larger than a threshold value, an operational frequency of the outer data signal is reduced.