A novel system of implementing target identification with hyperspectral imaging system based on acousto-optic tunable filter (AOTF) was proposed. The system consists of lens, AOTF, AOTF driver, CCD and image collection installation. Owing to the high spatial and spectral resolution, the system can operate in the spectral range from visible light to near infrared band. An experiment of detecting and recognizing of two different kinds of camouflage armets from background was presented. When the characteristic spectral wave bands are 680nm and 750nm, the two camouflage armets exhibit different spectral characteristic. The target camouflage armets in the hyperspectral images are distinct from background and the contrast of armets and background is increased. The image fusion, target segmentation and pick-up of those images with especial spectral characteristics were realized by the Hyperspectral Imaging System. The 600nm, 680nm, and 750nm images were processed by the Pseudo color fusion algorithm, thus the camouflage armets are more easily observed by naked eyes. Experimental results confirm that AOTF hyperspectral imaging system can acquire image of high contrast, and has the ability of detecting and identification camouflage objects.