The invention discloses a low strain detection method based on frequency domain analysis. The low strain detection method based on frequency domain analysis comprises the steps of performing fast Fourier transform on a signal, analyzing a frequency spectrum, and selecting proper hammering and sensor installing methods; timely performing Fourier transform on a time domain signal when in detection, judging whether hammer frequency is suitable in the frequency spectrum, and guiding and selecting the hammering mode and the sensor installing mode when in detection; and when the detection signal is in an oscillation waveform, analyzing whether the oscillation signal is interference caused by improper excitation or is caused by reflection of a pile body defect. When the method provided by the invention is applied to the detection of a foundation pile low strain reflected wave method, the Fourier transform is performed on the signal in time, and the frequency spectrum is analyzed to select the proper hammering and sensor installing methods; and when the oscillation signal is generated, time domain analysis is combined with frequency domain analysis to perform proper filtering, suppress interference and judge comprehensively, and thus accuracy of completeness judgment of a pile body is improved.