Due to the affine least squares matching method is unable to select the matching window adaptively without the initial parameter, an adaptive window least squares matching method based on local shape estimation was proposed. First, LOG (Laplacian of Gaussian)detector was used to detect feature points and characteristic scale; second, the second-order moment matrix in the neighborhood of feature points according to the characteristic scale was calculated; finally, the local shape estimation was applied to the adaptive selection of the initial matching window for affine iterative least squares method. The experiment results show that, the method can accurately select effective matching area under the larger affine deformation, avoiding iterative convergence problem caused by the window content differences. 