The invention provides a frequency deviation estimation method used in the uplink of a wireless communication system. The method comprises the following steps: step S102, a reference mark is constructed in the frame structure of a transmitted signal at the transmitting terminal, and the transmitted signal is transmitted to a receiving terminal; step S104, after time synchronization is conducted to the received signal, the receiving terminal extracts the reference mark from the signal; step S106, phase comparison is made between the reference mark from the transmitting terminal and the reference mark extracted at the receiving terminal, and the comparison result is recorded into a phase deviation information value; and step S108, the frequency deviation estimation value is determined according to the length of the reference mark of the transmitted signal and the phase deviation information value. While ensuring the synchronization precision, the method does not increase the resource burden of the system, and the operand is very small. Therefore, the method is favorable for projects to be realized.