Objective: To describe the prevalence of permanent tooth caries and associated factors among junior high school students in Haikou, and to provide reliable evidence for prevention and control of caries. Methods: A total of 3 573 students from 8 junior high school in Haikou City and towns were selected by the methods of clustered sampling survey. Questionnaire survey and oral health examinations were conducted to analyze the caries rate, mean decayed missing filled tooth (DMFT), filling rate, pit and fissure sealant rate. Logistic regression was used to analyze the influencing factors of caries in permanent tooth. Results: Among the surveyed junior high school students, the caries rate was 47.32%( n =1 691), the mean DMFT was 1.51. The caries rate and mean DMFT were higher in female students (49.59%) than in male students (44.95%), and higher in towns (50.77%) than in urban areas (44.04%), the difference were statistically significant ( χ 2=16.25, 7.72, P <0.05). The filling rate and pit and fissure sealant rate among junior high school students in Haikou were 17.13%, 6.27% respectively. The filling rate and pit and fissure sealant rate were higher in urban areas (18.97%, 7.17%) than towns (15.76%, 5.33%), the difference were statistically significant ( χ 2= 9.57, 5.13, P <0.05). The multivariate Logistic analysis showed that female student, town residence, daily consumption of sweets or sugary drinks (≥1 time), bedtime snack were risk factors for junior high school students suffering from permanent dental caries( OR =1.41, 1.45, 2.63, 2.09, 1.53), while using fluoride toothpaste daily, oral education in school were protective factors( OR =0.44, 0.34)( P <0.05). Conclusion The caries rate of permanent teeth among junior high school students in Haikou is at high level, but the filling rate of caries and pit and fissure sealant rate are lower. The prevention and treatment of dental caries should be carried out in high risk students, and oral health education in school is also needed to improve the oral health level of junior high school students.