Objective To explore the statues of sub-health and study the influence of family and school atmosphere to it among the junior middle school students. Methods 460 students of a junior middle school in Taiyuan collected by multistage sampling were investigated with the multidimensional sub-health questionnaire of adolescents,the Chinese version of the family environment scale,and the school life satisfaction rating questionnaire. Results The incidence of sub-health among junior middle school students was 47.2%.There was no significant difference between the boy and the girl students about the incidence of sub-health(P>0.05).The incidence of sub-health of the students in grade three was higher than that in the lower grades(P<0.05).Multiple logistic regression analysis showed that conflict,achievement orientation in family were risk factors of sub-health,while cohesion,active-recreational orientation,etc in family and higher school life satisfaction were protective factors of sub-health. Conclusion Effective measures should be taken to improve the family and school atmosphere in order to prevent the junior middle school students from sub-health.