The invention discloses a sub-pixel level image registering method and system. The method adopts a registering strategy from rough to fine in stages. In the rough registration stage, image features are extracted, and a target image and an original image are evenly blocked according to the inconsistent transformation conditions of the different areas of the images, the unequal importance is distributed to the image features according to the weight, a transformation model is fitted, and the rough registration can be efficiently completed; and in the fine registration stage, each image block is subjected to overlapped regular division, the transformation model is modified by taking the coefficients solved in the rough registration stage as the initials, the optimal transformation model of each image block is obtained according to the similarity measurement, the pixel offset amount of the overlapped areas is weighted and fine-adjusted to realize the uniform transition of the adjacent blocks and eliminate the influence of small offset on the registration accuracy, and the image fine registration can be completed in high precision. The method and the system of the invention realize the high-precision sub-pixel registration of the images while accurately express the inconsistent transformation conditions of the different areas of the images.