Excellent auto-focusing technology is necessary for measuring the diameter of the optical fiber accurately, stably, efficiently and real-time, especially the coating layer peeled optical fiber by microimaging. Focusing window selection is the premise of auto focusing. In order to avoid the influence of the intermediate transmission or the diffraction light band on the optical fiber side imaging, an improved method to select the localized elliptical window is proposed. At the same time, the effects of different window shapes on the clearness evaluation and calculation speed are also compared. By applying the method to the measurement of 125 μm standard optical fiber, we find that the standard error is within 0.3 μm and the measurement accuracy is increased by an order of magnitude compared to the micron scale of the VM2.22 precision measurement software. The method is practical, fast and versatile, and can be used as an effective method for automatic focusing window selection.