The invention relates to the field of digital wireless communication and discloses a frequency shift estimation method and system for coherent demodulation frequency shift keying modulating signals. According to the method and the system, prefix signals of GFSK (Gaussian Frequency Shift Keying)/FSK (Frequency Shift Keying) signals are designed to a string of fixed-length codes with altering 0 and 1, and according to the prefix signals, an ideal receiving signal c(i) can be completely eliminated from an x(i) under the condition that a receiver does not need to copy the ideal receiving signal c(i), thereby solving the problem that as the frequency modulation index of the GFSK/FSK signal can not be obtained accurately and can change along with time and temperatures, a receiving terminal can not accurately copy the ideal receiving signal c(i), so as to improve the accuracy of the frequency shift evaluation. Therefore, by virtue of the iteration-combination of frequency evaluation results of R(N), R(2N),..., R (KN), the phase ambiguousness caused by the large frequency shift can be eliminated, and the precision of the frequency shift evaluation can be improved further.