The invention relates to a frequency offset estimating method and a system thereof. The method comprises the steps of performing gaining on a to-be-measured signal according to the to-be-measured signal after bit decision, and obtaining a frequency offset component of the to-be-measured signal according to the gained to-be-measured signal. According to the frequency offset estimating method and the system thereof, gaining is performed on the to-be-measured signal according to different transmission periods of the to-be-measured signal after bit decision, and furthermore score elimination is performed on the to-be-measured signal after gaining for eliminating +/- code flows and a Gaussian white noise in a discrete time domain signal output from a demodulation module for acquiring the frequency offset component of the to-be-measured signal, thereby saving hardware resource and energy, and improving frequency offset correction efficiency and precision under a precondition of low cost.