The patient health questionnaire-9 (PHQ-9) is widely utilized in assessing individuals' depression levels. Nevertheless, research regarding its factor structure and measurement invariance remains inadequate. The aim of this study was to delve into the factor structure of the PHQ-9 and to further investigate its measurement invariance across gender and age as a prerequisite for its use in cross-group comparisons. A confirmatory factor analysis (CFA) was conducted on 7422 Chinese students to assess the best-fitting factor structure of the PHQ-9. Furthermore, a serial CFA was undertaken to investigate measurement invariance across genders and age groups. CFA confirmed the two-factor model with the three items "sleep disturbance," "fatigue," and "appetite change" loading on somatic factor, and the other items loading on cognitive/affective factor as the best-fit structure. Findings demonstrated that the PHQ-9 had measurement invariance across gender and age. CFA and measurement invariance results support the application of the PHQ-9 for assessing an individual's depression.