Currently, research in sexual behavior and awareness in female Chinese college students (FCCSs) is limited, particularly regarding the difference and the influencing factors between students from rural areas and urban areas. To fill the gap in available data, a cross-sectional study using anonymous questionnaires was conducted among 3193 female students from six universities located in Beijing, Shanghai, and Guangzhou, China, from February to June, 2013. Of the 2669 respondents, 20.6% and 20.9% of the students from urban and rural areas, respectively, reported being sexually experienced. The proportion of students who received safe-sex education prior to entering university from rural areas (22.4%, 134/598) was lower (P < 0.0001) than the proportion from urban areas (41.8%, 865/2071). Sexual behavior has become increasingly common among FCCSs, including high-risk sexual behavior such as unprotected commercial sex. However, knowledge concerning human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) transmission and the risks is insufficient, particularly for those from rural areas, which is a challenge for HIV/AIDS control in China. The Chinese government should establish more specific HIV/AIDS prevention policies for Chinese young women, strengthen sex education, and continue to perform relevant research.