The present field investigation sought to explore the relationship between mental health and abnormal menstruation in female middle school students from post-earthquake Wenchuan following the 2008 Sichuan earthquake (the earthquake's epicenter was in Wenchuan Couty, Sichuan Province). A total of 587 female middle students from post-earthquake Wenchuan were given the PCL-C, SCL-90, and a menstruation questionnaire. Outcomes were measured by diagnostic criteria. The general incidence of PTSD was 60.8%, and D symptoms were the most prevalent PTSD symptoms (49.6%). Of symptoms indicated by the Symptom Checklist, obsessive-compulsive traits were most prevalent (94.6%), followed by interpersonal sensitivity (91.9%). The incidence of abnormal menstruation was 76.6%. Incidence of abnormal menses among students who screened positive for PTSD was significantly higher than among students who did not (chi2 = 4.015, p = 0.045). The incidence of abnormal menses was higher among students who screened positive for somatization, obsessive-compulsive traits, phobic anxiety, and diet and sleep disorders than among those who did not (p < 0.05). In conclusion, there was a relationship between mental health and physical health in female middle school students in a post-earthquake area. A higher incidence of abnormal menstruation may occur in students with PTSD, somatization disorder, obsessive-compulsive disorder, phobic anxiety, and diet and sleep disorders. Therefore, psychological intervention is particularly necessary for female students who have survived a natural disaster like an earthquake.