The small imaging size of targets over long distances results in the loss of geometry and spatial features. Current methods are subject to sampling limitations and cannot accurately capture the spatial features of sub-pixel targets. This paper proposes a method to accurately locate and extract the fine spatial features of sub-pixel targets through aperture coding and micro-scanning imaging. First, the formation mechanism of imaging features for sub-pixel targets is analyzed. Second, the optical aperture is anisotropically coded in different directions to modulate the spreading spots of the target. The primary spreading direction and the center of the anisotropic spreading spots are extracted. The contour and the location of the target are determined from the spreading length and the intersections of the primary spreading directions. Then, the target is sampled by different detector units through various micro-scanning offsets. The pixel units containing different sub-pixel components of the target after offset are determined based on the location results. The fine spatial distribution of the sub-pixel target is reconstructed based on the intensity variations in the pixel units containing the target. Finally, the accuracy of the sub-pixel target fine spatial feature extraction method is validated. The results show a sub-pixel localization error of less than 0.02 and an effective improvement of the sub-pixel target spatial resolution. This paper provides significant potential for improving the ability to capture spatial features of targets over long distances.