Objective To investigate the current situation of perimenopausal syndrome(PMS) among clinical nurses in different levels of hospitals in Chongqing, to analyze the influencing factors and differences, and to provide reference for a boost of physical and mental health of perimenopausal nurses. Methods A total of 933 nurses from 13 tertiary hospitals, 24 secondary hospitals and 42 primary hospitals in Chongqing were selected by stratified random sampling. The Kupperman Self-rating Menopausal Symptoms Scale, Social Support Scale, Family Care Index and Nursing Work Environment Scale were used for survey. Results There were no significant differences in the incidence rate and symptom severity of perimenopausal syndrome among clinical nurses in different levels of hospitals in Chongqing (P>0.05 for both). Logistic regression analysis showed that chronic disease, exercise less than 6 times per week and being in menopause were risk factors of PMS of clinical nurses in primary/secondary hospitals, while sufficient manpower was a protective factor (P<0.05 for all). In tertiary hospitals, exercise less than 6 times per week, being in menopause，low/medium level of social support and impaired family care were risk factors for PMS of clinical nurses, while basic protection was a protective factor (P<0.05 for all). Conclusion The occurrence of PMS among clinical nurses in different levels of hospitals in Chongqing was not optimistic, and the influencing factors varied. Targeted and effective intervention measures should be taken by nursing managers to promote the physical and mental health of perimenopausal clinical nurses.