Objective: To investigate the awareness of pubertal knowledge and its influencing factors among primary school students in Chinese rural areas, and to provide evidences for improving awareness level and popularizing scientific, reasonable, and suitable sex education. Methods: Sixteen primary schools consisting of rural registered students in Guizhou and Anhui Province were selected by multi-stage cluster sampling method, and a questionnaire survey for 2 506 senior students (grade five and six) was conducted to explore the awareness of pubertal knowledge and its influencing factors among primary school students in Chinese rural areas. Results: The total awareness rate of pubertal knowledge was 62.7% among primary school students in Guizhou and Anhui rural areas, and the awareness rates were relatively low for the questions about the difference between male and female pubertal development and understanding of sexual attitude; female students, only-child students and grade six students got a bit better awareness of pubertal knowledge than male students, non-only-child students and grade five students respectively; grade[OR=0.72(0.61-0.86)], peer acceptance [OR=0.70(0.53-0.96)], family intimacy [OR=0.75(0.63-0.88)] had effect on awareness of pubertal knowledge. Conclusion The awareness of pubertal knowledge among primary school students in Guizhou and Anhui rural areas need further improvement, especially for male students, non-only-child students and grade five students in the questions about the difference between male and female pubertal development and understanding of sexual attitude. It is necessary to improve the awareness of pubertal knowledge by enhancing peer acceptance, promoting family intimacy, and popularizing scientific, reasonable, and suitable sex education.