The invention provides a vibration source identification method and system based on a signal frequency domain feature. The method comprises the steps that the vibration signals of the current vibration source at a number of alarm points are acquired; each vibration signal is preprocessed; energy detection is carried out on each vibration signal according to a standard signal to acquire the identification signal of the current vibration source; the correlation coefficient between each identification signal and the standard signal under different working conditions is acquired according to the signal frequency domain feature; and when knocking vibration signals are in the identification signal and the number of the knocking vibration signals is more than a second threshold, the current vibration source is identified as a knocking vibration source. The system comprises a vibration signal acquisition unit, a preprocessing unit, an energy detection unit, a correlation coefficient acquisition unit and a knocking vibration source identification unit. According to the invention, the knocking vibration signals can be accurately identified according to the signal frequency domain feature; the identification process is quick and effective; a reliable vibration source determining basis is provided for a control center; and the control center can make accurate and timely response according to the type of the vibration source.