A new frequency domain method for charged particle identification, called Frequency Ratio Analysis (FRA), is proposed by analyzing the frequency spectra of proton pulses and alpha pulses acquired from a totally depleted Si detector. Identification performance of the FRA method is evaluated and compared with two time domain methods, the current pulse amplitude method and the second moment method. The results show that the FRA method is not only feasible and effective but also superior to the two time domain methods, as it achieves an obvious increase in value of the figure-of-merit (FOM).