Objective: To analyze the one year follow up changes and influencing factors of anisometropia among primary school students in Beihai, so as to provide data support for formulating targeted prevention and control strategies. Methods: In 2023 and 2024, visual acuity and refractive screening were conducted on primary school students in Beihai. A cohort matching method was used based on unique identifiers to link data from 2023 (baseline) Grades one to five with those from 2024 (follow up) Grades two to six, obtaining a total of 59 743 complete datasets. McNemar test and generalized estimating equations(GEE) model were employed to analyze the changing patterns of anisometropia. Results: The detection rate of anisometropia among primary school students in Beihai increased from 10.88% in 2023 to 12.30% in 2024 ( χ 2=97.12, P <0.01). Among them, the detection rate in Grade 1 decreased from 8.82% in 2023 to 7.50% in 2024, Grade 3 increased from 10.15% to 11.52%, Grade 4 increased from 12.10 % to 15.22%, Grade 5 increased from 14.61% to 17.88% ( χ 2=16.51,18.03,95.52,95.95,all P <0.05). The GEE results showed that the risk of anisometropia development was higher in girls than in boys ( OR =1.15), the risk of anisometropia increased by 16% with each 1 year increment in age ( OR =1.16) among primary school students, the risk of anisometropia development in Grade 5 was 2.20 times higher than that in Grade 1 ( OR =2.20)(all P <0.05). In lower grades, only the baseline anisometropia status in lower grades had a statistically significant effect on anisometropia among primary school students( OR =59.09), while the positive effects of gender and age difference gradually emerged and strengthened in middle and higher grades (all P ＜0.05). Conclusions The detection rate of anisometropia among primary school students in Beihai shows dynamic changes and influencing factors vary by grade level. It is necessary to develop stratified prevention and control strategies tailored to different grades.