A clock adjusting device includes an oscillator, a first counter, a second counter, a count comparator and a threshold comparator. The oscillator transmits an operation clock signal. The first counter counts a reference clock signal, to obtain a reference clock count value. The second counter counts the operation clock signal to obtain an operation clock count value. The count comparator compares the reference clock count value with the operation clock count value, to obtain a candidate correction value. The oscillator adjusts the operation clock signal according to an output correction value. The threshold comparator compares the candidate correction value and an updated threshold. When the candidate correction value is lower than the updated threshold, the candidate correction value is used as the output correction value, and when the candidate correction value exceeds the updated threshold, a current correction value is used as the output connection value.