Objective: To understand the current status of malnutrition, depressive symptoms, and their coexistence among middle school students, so as to provide references for exploring the "comorbidity-common cause-common prevention" model for these conditions. Methods: In September 2023, a stratified random cluster sampling method was adopted to select 88 594 students from junior high schools, regular high schools, and vocational high schools in 12 leagues/cities (covering 103 banners/counties) of Inner Mongolia Autonomous Region. Physical examinations were conducted to collect data on malnutrition, and the Center for Epidemiologic Studies Depression (CES-D) Scale was used to assess depressive symptoms. The Chi-square test and multivariate linear stepwise regression analysis were employed to analyze the related factors of malnutrition, depressive symptoms, and their coexistence. Results: In 2023, the detection rates of malnutrition, depressive symptoms, and their coexistence among middle school students in Inner Mongolia were 4.60%, 21.85%, and 0.90%, respectively. There were statistically significant differences in the detection rates of malnutrition, depressive symptoms, and their coexistence among middle school students of different genders, monitoring sites (except for malnutrition), and school stages ( χ 2=4.95-817.39, all P <0.05). The results of the multivariate Logistic regression analysis showed that high school students，drink sugar sweetened beverages ≥1 time per day and those with Internet addiction had higher risk of coexisting malnutrition and depressive symptoms [ OR (95% CI )=1.38 (1.04-1.83), 1.46 (1.20-1.78), 2.28 (1.90-2.74), respectively, all P <0.05 ]. The risk of coexistence was lower among female students, those who ate fresh fruits at least once a day, those who engaged in moderate-to-vigorous physical activity for ≥1 time/day, those who engaged in moderate-to-vigorous physical activity for ≥1 hour/day on ≥5 days/week, those who did not use cough syrup without therapeutic need, those who did not use sedative hypnotic drugs without medical advice, and non-drinking students [ OR (95% CI )=0.84 (0.73-0.98), 0.77 (0.66-0.89), 0.82 (0.68-0.98), 0.66 (0.53- 0.80 ), 0.57 (0.41-0.78), 0.63 (0.53-0.72), respectively, all P <0.05]. Conclusions The occurrence of undernutrition, depressive symptoms, and their coexistence among middle school students in Inner Mongolia can t be ignored. Schools, the government and society should implement a strategy aimed at concurrent prevention of multiple conditions through comprehensive interventions.