In China, food safety problems have occurred frequently in the past ten years, causing great concern for the public. Adolescents, with higher exposure to problematic food, represent a unique target for interventions aimed at risk reduction. To understand their food safety knowledge, attitude and practice, a cross-sectional survey using paper questionnaire was carried out among 4,220 students (median age of 14 years, 50.3% females) from nine secondary schools in 3 districts of Beijing. The findings showed that the majority of respondents (42.0%) had a high knowledge level. Significant association was found between food safety knowledge score (median = 11, IQR:9–13) and demographic characteristics of region, school type, residence type, habit of smoking and alcohol use, academic record and parents’ education background. In terms of attitude and practice, only 17% of those surveyed regarded China’s food safety situation as good, 53.6% regarded it as worrying; almost all students (96.5%) did pay attention to food safety; 95.3% of the students had worried about the safety of the food provided by the small restaurants and street peddlers, but in reality, as many as 69.4% often or occasionally bought food from peddlers around their campuses and nearly half continued the consumption of such food in spite of worrying about its safety problems. Overall, the food safety knowledge among Beijing secondary school students was relatively good. They did not show much confidence in the country’s food safety situation, but many aware of the safety issues did not bother to change or take action. The study suggests that more systematic and targeted education on food safety is necessary for this age group.