Objective: To investigate the prevalence of co-occurrence of common diseases among junior high school students in Yunnan Province and to identify latent comorbidity patterns and analyze their associated factors, so as to provide evidence for the comprehensive prevention and control of common diseases among students. Methods: From September to November 2025, a stratified cluster sampling method was employed to survey 71 791 students in grades 7-9 recruited from 258 junior high schools in Yunnan Province. Information on six common diseases, including screening myopia, dental caries, overweight/obesity, malnutrition, elevated blood pressure, and abnormal spinal curvature, was collected through physical examinations and questionnaire surveys, along with data on demographic characteristics, physical activity, and sleep. Latent class analysis (LCA) was used to identify comorbidity patterns of common diseases, and multinomial Logistic regression was performed to analyze the factors associated with each pattern. Results: The detection rates of screening myopia, dental caries, overweight/obesity, elevated blood pressure, malnutrition, and abnormal spinal curvature among junior high school students were 65.2%, 62.1%, 22.4%, 10.9% , 8.2%, and 5.7%, respectively. LCA identified three latent comorbidity patterns of common diseases: a high prevalence screening myopia-dental caries-spinal curvature abnormality pattern (C1, 63.8%), an overweight/obesity elevated blood pressure pattern (C2, 24.1%), and a relatively low burden pattern (C3, 12.0%). With C3 as the reference, multinomial Logistic regression showed that girls were more likely than boys to be assigned to C1 and C2 [ OR (95% CI )=2.12(2.02-2.23), 1.31(1.23-1.38)]; non-Han students were less likely than Han students to belong to C1 and C2 [ OR (95% CI )=0.88(0.83-0.92), 0.81(0.77-0.86)]; students in grades 8 and 9 were more likely than those in grade 7 to belong to C1 and C2, with the highest likelihood observed among grade 9 students [ OR (95% CI )=1.43(1.35-1.52), 1.27(1.19-1.36)]; insufficient sleep was associated with increased odds of belonging to C1 and C2 [ OR (95% CI )=1.15(1.09-1.22), 1.25(1.18-1.33)] (all P <0.05). Compared with students who engaged in outdoor activities during breaks, those who stayed indoors, either inside the teaching building but outside the classroom or inside the classroom, were more likely to belong to C1 [ OR (95% CI )=1.09(1.02-1.16), 1.17(1.09-1.26)] and C2 [ OR (95% CI )=1.13(1.05-1.21), 1.25(1.15-1.35)]; students not living with their parents were less likely to belong to C1 and C2 [ OR (95% CI )=0.83(0.77-0.90), 0.74(0.68-0.81)] (all P <0.05). Conclusions The co-occurrence of common diseases is relatively prominent among junior high school students in Yunnan Province, with distinct latent stratification patterns. Tiered and precise comprehensive interventions should be implemented targeting key populations to promote the prevention and control of common diseases among students.