The invention discloses a harmonic frequency identifying and rejecting method based on spectroscopic derivatives and frequency hurdle seams. The method is characterized by including the following steps: calculating a first order derivative or second order derivative of a vibration signal power spectrum G([Omega]), and obtaining a spectrum abrupt change degree ab([Omega]) or a quickness ag([Omega]); setting thresholds of the spectrum abrupt change degree or the quickness as ab-max and ag-max respectively; finding a frequency point [Omega]i in an ab([Omega]i)=ab-max position or ag([Omega]i)=ag-max position; finding a frequency point [Omega]j the first spectrum abrupt change degree of which is negative or the third quickness of which is negative after the frequency point [Omega]i, the frequency point [Omega]j being a harmonic frequency [Omega]h; and building frequency hurdle seams and rejecting all harmonic frequencies through the identified harmonic frequency [Omega]h, and obtaining the real inherent frequency of a mechanical structure. The method is high in detection accuracy, is capable of obtaining the inherent frequency of a mechanical structure when the mechanical structure is in a working state, and provides a powerful means for identifying and monitoring a mechanical structure on-line and identifying structural damage of a mechanical structure.