The characteristics of an acousto-optical modulator (AOM) with cross-talks among its diffracted beam are proposed and verified theoretically and experimentally. The cross-talks cause intensity modulation items and the frequencies are harmonics of the driving frequency in each diffracted beam. The drift of the incident beam on an AOM will cause a frequency drift in its diffracted beams. The influences on the measuring accuracy of an AOM heterodyne interferometer are analyzed in detail. Methods to eliuminate the influences are proposed and identified: employing two AOMs and obtaining its reference signal from the interferometer. The AOM heterodyne interferometer can be used in the case of the accuracy beyond nanometer.