Registration of electron microscopy (EM) images is one of the most important steps in reconstructing neurons. Image registration algorithm based on SIFT have been widely used in the EM image registration. But SIFT matching procedure both costs a lot of time and introduce massive false matches. In this paper, we propose an improved EM image registration method using the scale information of SIFT keypoints. In the feature matching procedure, our method saves up to 45.8% of the computation time compared to SIFT. We also added a preprocessing procedure for RANSAC to eliminate false matches in small-scale matches sets. Experimental results show that the method improves the accuracy of results on every test EM image set while highly reducing the registration time.