Nonuniformity in FPAs (focal plane arrays) is a common, although undesirable, characteristic arising from small differences in the responsivity of individual detectors. Now there are many scene-based nonuniformity correction algorithms. In these correction algorithms, interframe registration based nonuniformity correction algorithm is a principal type. The core of interframe registration based nonuniformity correction algorithm is accurate image registration. However, because of the existence of the nonuniformity, the values of the adjacent columns or rows of the image with noise are so close that it is difficult to distinguish them. We find it is difficult to achieve the corresponding rows or columns registration between two frames accurately. It will lead to the wrong registration that will affect the nonuniformity correction effect. In this method, we propose a nonuniformity correction algorithm based on subspace projection registration. By projecting the rows and columns of the image on to their corresponding subspace respectively, we can realize the dimension reduction of the row space and the column space. As a result, the value differences between the adjacent rows or the adjacent columns of the image can be amplified. Then the algorithm can identify the corresponding rows and columns between two frames, enabling accurate image registration. Experiments demonstrate that our algorithm achieve accurate image registration and outstanding correction effect.