The Acousto-Optic Tunable Filter (AOTF) is an electronically tunable optical filter based on Acousto-optic effect and has its own special compared with other dispersive parts. Imaging spectrometer based on acousto-optic tunable filter (AOTF) is a useful high-spectral technology, especially in deep space exploration applications because its characteristics of staring imaging, electronic tunable spectral selection and simple structure. Because the diffraction of light in AOTF filters is dependent on both wavelength and angle of incidence, the Spectral and geometrical calibration must therefore be performed over the entire spectral range of AOTF hyper-spectral imaging systems. In this paper, the dispersive principle of AOTF is introduced firstly and its application predominance in space-based spectral detection is analyzed. Then, a method for calibration of acousto-optic tunable filter (AOTF) hyper-spectral imaging systems is proposed and evaluated. This paper introduces the calibration of a VIS-NIR Imaging Spectrometer (VNIS) by the method. The VNIS is a payload instrument for lunar detection and provides programmable spectral selection from 0.45 to 0.95μm. The results indicate that the method is accurate and efficient. Therefore, the proposed method is suitable for spectral and geometrical calibration of imaging spectrometers based on AOTF.