Objective To analyze the specific causes of rejection of the students for navy teenager aviation school due to ophthalmic problems in entrance physical examination, so as to provide evidence for exploring the ophthalmic standard and scientific testing methods to improve the quality of enrollment physical examination. Methods A total of 3 583 male junior high school graduates, aged 14-16 years, received physical examination for 14 navy teenager aviation schools in 2019. The participating medical staff and 14 schools were randomly divided into three groups for the physical examination. The causes of rejection due to ophthalmic problems were classified and sorted, and the rejection rates and rejection causes were compared between the three physical examination groups and 14 schools. Results Altogether 3 583 students received ophthalmic physical examination, and 1 657 were rejected, with a rejection rate of 46.25%. The rejection rates in the ophthalmology department in the three groups were 39.18% (552/1 409), 45.26% (482/1 065) and 56.18% (623/1 109), respectively, showing significant differences between the three groups (χ²=72.74, P<0.05). The top three causes of rejection were far vision deficiency (34.25%, 1 227/3 583), latent deviation excess (2.32%, 83/3 583), and refractive excess (2.04%, 73/3 583). Among the potential students of the 14 schools, the difference in rejection rate by far vision deficiency was greater (14.00%-59.50%). Other items with great differences among different schools included latent deviation excess (0.41%-6.33%), refractive excess (0-8.00%), eye pressure excess (0-4.50%), and corneal topographic map abnormality (0-5.98%). Conclusion The rejection rate in ophthalmology department is high during entrance physical examination of students for navy teenager aviation school, and there are differences between different groups and different schools. To accurately understand the standards and optimize the physical examination process are keys to improve the quality of physical examination of students for navy teenager aviation schools.