Microscopic visual measurement is one of the main methods used for precision measurements. The observation morphology and image registration algorithm used in the measurement directly affect the accuracy and speed of the measurement. This paper analyzes the influence of morphology on different image registration algorithms through the imaging process of surface morphology and finds that complex morphology has more features, which can improve the accuracy of image registration. Therefore, the surface microstructure of ultra-precision machining is an ideal observation object. In addition, by comparing and analyzing the measurement results of commonly used image registration algorithms, we adopt a method of using the high-speed SURF algorithm for rough measurement and then combining the robust template-matching algorithm with image interpolation for precise measurements. Finally, this method has a repeatability of approximately 54 nm when measuring a planar displacement of 25 μm.