Abstract: Objective To understand their situation of sub-health by investigating the middle school students of three areas in China, and to provide the reference for relevant measures and promoting middle school students' health.Methods A multi-dimensional self-administered questionnaire was used to investigate 3 026 middle school students selected from Tibet, Shanxi and Guangzhou from 2012 to 2013 by two-stage sampling method.Results The detection rate of psychological sub-health was 11.12%in junior middle school students and 17.5% in high middle school students.Overweight burden of study, spending over 4 hours on internet, drinking, and imbalanced diet were the risk factors of psychological sub-health in junior middle school students (OR =1.942, 2.298, 1.919, 1.735).Exercise, adequate sleeping time, having a large number of friends and seeking help were the protective factors of the state of sub-health in junior middle school students (OR = 0.522, 0.189, 0.275, 0.570).Grade, lack of sleep, overweight burden of study, going home for less than one time a week, lack of exercise, smoking, drinking, lack of friends and introversion were the risk factors of psychological sub-health in high middle school students (OR = 1.728, 9.459, 2.427, 2.478, 2.472, 2.138, 2.344, 10.324, 1.547).Boy students, families in the villages and towns, seeking help were the protective factors of psychological sub-health in high middle school students (OR = 0.679, 0.588, 0.378).Conclusion It suggests that the comprehensive prevention and control measures should be taken, the risk factors be excluded and the protective factors be taken, the state of the psychological sub-health can be effectively prevented and controlled, and the health growth of the middle school students can be maintained.