The present invention provides a gear fault detection method on the basis of multi-position turning angle signals of encoders. The gear fault detection method on the basis of multi-position turning angle signals of encoders comprises the following steps: axial angle encoders are installed at the power input end and the power output end of a gear case; turning angle signals of the axial angle encoders are collected by the encoders at the input shaft end and the output shaft of the gear case; the turning angle signals are processed and reference points of square wave periods in the signals are searched, the period timing length of each square wave in the signals are counted, the period fluctuation time series are reconstructed according to the number of periods of each square wave, and frequency spectrums of the period variation time series signals; and finally, characteristic frequency components of fault gears are calculated according to the rotating speed of the input shaft and the design structure of the gear case, and when fault characteristic components and high order harmonic components thereof are existed in the frequency spectrum, it is determined that flex cracking or an abnormal failure of the gear case happens. The gear fault detection method on the basis of multi-position turning angle signals of encoders has high recognition rate of operation failures of a gear, and contributes to rapidly and accurately determining the operating state of a gear case.