Imaging spectrometer based on acousto-optic tunable filter (AOTF) is a novel hyperspectral imaging system. In order to rectify the non-uniformity of radiation sensitivity on different waveband, especially the low signal-to-noise (SNR) in low-light conditions, the electron-multiplying CCD (EMCCD) sensor was proposed. The noise of AOTF imaging spectrometer was analyzed in both normal and EM modes of the CCD sensor with derived SNR calculating model which has been experimentally validated. On that basis, a new evaluation method of the dynamic range in EM mode and a novel method of calculating spectral radiance at the entrance aperture were adopted. The experimental result shows that the theoretic SNR models are fit, and better selection of EM mode is effective to improve the SNR and non-uniformity of radiation sensitivity in low light level conditions.