In order to carry out high precision detection of frequency shift error of the acousto-optical modulator (AOM), a heterodyne interferometer detection method and an experimental system are designed. By measuring the frequency of the heterodyne interference signal, the actual difference frequency of the double AOM can be obtained. Spectrum correction algorithm using Hanning window is used for precise frequency correction. The relationship between detection accuracy of the difference frequency and sampling number by signals with different SNR is simulation analyzed, and the difference frequency of a pair of AOMs by designed experimental system is also detected. The simulation and experimental results show that the detection accuracy of the method used for difference frequency of double AOMs is better than 2 Hz. The method can provide valid reference for error analysis of high precision heterodyne detection system for application.