This paper presents a non-rigid registration method for the restoration of double-sided historical manuscripts. Firstly, the gradient direction maps of the two images of a manuscript are examined to identify candidate control points. Then the correspondences of these points are established by minimizing a disimilarity measure consisting of intensity, gradient and displacement. To fully capture the spatial relationship between the two images, a mapping function is defined as the combination of a global affine and local b-splines transformation. The cost function for optimization consists of two parts: normalized mutual information for the goal of similarity and space integral of the square of the second order derivatives for smoothness. To evaluate the proposed method, a wavelet based restoration procedure is applied to registered images. Real documents from the National Archives of Singapore are used for testing and the experimental results are impressive.