A method of a phase-locked loop circuit includes: using a phase detector to generate a charging current signal according to an input frequency signal and a feedback signal; limiting a voltage level corresponding to the charging current signal in a voltage range according to a prediction signal to generate a digital output; performing a low-pass filter operation according to the digital output; generating a digital controlled oscillator (DCO) frequency signal according to an output of the loop filter; generating the feedback signal according to the DCO frequency signal; generating a phase signal, which indicates accumulated phase shift information, according to information of the feedback circuit and fractional frequency information; and, generating the prediction signal according to the phase signal.