A dual sensor imaging system and an imaging method thereof are provided. The method includes: identifying an imaging scene; controlling a color sensor and an IR sensor to respectively capture color images and IR images by adopting capturing conditions suitable for the imaging scene; calculating a signal-to-noise ratio (SNR) difference between each color image and the IR images, and a luminance mean value of each color image; selecting the color image and IR image captured under capturing conditions of having the SNR difference less than an SNR threshold and the luminance mean value greater than a luminance threshold to execute a feature domain transformation to extract partial details of the imaging scene; and fusing the selected color image and IR image to adjust the partial details of the color image according to a guidance of the partial details of the IR image to obtain a scene image with full details.