In order to obtain high signal-to-noise ratio (SNR) tissue images with deeper imaging depths, the laser scanning confocal technology with the near infrared (NIR) fluorescence imaging is integrated and a laser scanning confocal NIR fluorescence imaging system based on requirements of NIR fluorescence imaging is established. A laboratory mouse injected with NIR fluorescence labeling LDS925 is placed in this system and a non-confocal NIR fluorescence image and a confocal NIR fluorescence images for the tail of laboratory mouse is obtained. The experimental results show that when evaluated by the mean square error and the peak valley (PV) value, the mean square error and the PV value is 864 and 102 respectively for the non-confocal NIR fluorescence image and 1459 and 255 for the confocal NIR fluorescence image, which further shows that the laser scanning confocal technology is applicable to the NIR fluorescence imaging, and the in vivo and high SNR tissue imaging with deeper imaging depths can be achieved.