Objective: To investigates the prevalence of depression and anxiety among middle school students at different times, and to provide a reference for mental health promotion among adolescents. Methods: A total of 1 505 middle school students, selected from Chongqing in 2021 by using multi stage stratified random sampling method, were surveyed by using the Center for Epidemiologic Studies Depression Scale(CSE-D) and Zung Self Rating Anxiety Scale (SAS). Results: At the beginning of the semester, 434(27.6%) and 601 students( 38.2 %) reported depressive and anxiety symptoms,respectively. While at the end of the semester showed that 463 cases (30.8%) were prone to depression, and 653 cases ( 43.4 %) reported depressive and anxiety symptoms,respectively. The detection rate of depressive symptoms at the end of the semester was significantly higher than that at the beginning of semester. (43.4%, 38.2 %, χ 2=8.55, P <0.05). Depressive of female students at the end of the semester( 52.8 %) was higher than that at the beginning of the semester(46.3%)( χ 2=6.19, P <0.05) The detection rate of anxiety symptoms in senior high school students at the end of the semester(44.9%) was significantly higher than that of at the beginning of the semester(28.6%) ( χ 2= 43.33 , P <0.01). No significant difference in anxiety symptoms boys and junior high school students between the beginning and the end of the semester ( χ 2=2.34, 0.71, P >0.05). Conclusion Substantial changes are observed in anxiety symptoms among female middle school students and depressive and anxiety symptoms among high school students in different periods of a semester. When investigating depression and anxiety of middle school students, time effect should be considered.