The reason why most ophthalmic medical research was carried out in mice is that the genes of mice and human are extremely similar. The retinal structure of a mature mouse has an important reference function for animals with ophthalmic diseases. Optical coherence tomography (OCT) is used to detect the delay of light echo time and obtain the layers of the detected tissue cells. The images of different layers of retina provided by OCT are closely related to histomorphology. The purpose of this paper is to study the application of OCT in fundus examination of mice and automatic segmentation and measurement of OCT images. First of all, due to the great difference in refractive structure between human and mouse eyes, this paper established a mouse retina OCT imaging device to study the image presentation effect of different sampling methods, so as to achieve the accurate display of mouse eye image; secondly, using the automatic segmentation and measurement technology of OCT image, the edge is detected step by step and the effect of image presentation is enhanced, and the contour is successfully extracted and compared with manual segmentation Finally, we compared the data obtained from mouse retinal tissue section and the data detected by OCT image. The final results show that the data detected by OCT imaging equipment can completely replace the data obtained by mouse tissue section, and even the improved OCT imaging device can detect the data that cannot be obtained by tissue section. This method not only improves the time-consuming and laborious disadvantages of manual mouse tissue sectioning, but also effectively promotes the establishment of ophthalmic disease model through the high-quality images obtained by the computer automatic processing of OCT imaging device.