A clock generation circuit and a clock adjustment method thereof are provided. The clock generation circuit includes a fixed clock source, a variable clock source, a timing adjustment circuit, and a pulse width signal generator. The fixed clock source generates a reference clock signal having a fixed frequency. The variable clock source receives a frequency setting signal to correspondingly generate an operational clock signal having a variable frequency. The timing adjustment circuit determines whether a frequency of the operation clock signal is N times of a target frequency according to the reference clock signal to set a frequency of the operation clock signal. The pulse width signal generator divides the operating clock signal to generate a pulse width modulation signal having the target frequency.