Purpose To study the association of myopia progression with the morphological changes of optic disc and beta-peripapillary atrophy (beta-PPA) in 8-11 years old primary school students. Methods This study was a prospective, school-based investigation. This study included 610 children (1008 eyes) who were continuously observed and had data available from 2016 to 2017 in the Sanhe Cohort Study of the Risk Factors for Myopia (SCSRFM). The children underwent a comprehensive eye examination including measurement of visual acuity, autorefractometry, and posterior segment of the eye. beta-PPA regions and optic disc ovality index were identified and measured on the fundus photographs. Results The prevalence of myopia was 72.62% (732/1008) in 2016. In myopic children, the prevalence of the vertical beta-PPA, the horizontal beta-PPA, and the oval optic disc were 75.68% (554/732), 75.96% (556/732) and, 11.61% (85/732) respectively. From 2016 to 2017, with the progression of vertical beta-PPA, horizontal beta-PPA, area of beta-PPA, and optic disc ovality index, the myopic diopter and the axial length (AL) were increased. The progression of horizontal beta-PPA was significantly correlated with the progression of myopic diopter and AL (all p < 0.05). The analysis on the distribution of progression rate of parameters in different groups found that the progression rate of horizontal beta-PPA, area of beta-PPA, and optic disc ovality index increased with the increase of the progression of diopter and AL. The progression of horizontal beta-PPA, area of beta-PPA, optic disc ovality index, and diopter in girls were greater than that in boys, and the progression of optic disc ovality index and diopter had a statistical significance (all p < 0.05). Conclusions The 1-year follow-up study of the third-grade primary school students showed that with the progression of myopia and the growth of AL, beta-PPA and optic disc ovality index also changed. There was a positive correlation between the change of beta-PPA and optic disc ovality index and the progression of myopia diopter and AL.