Background: The correlation between extension of the maxillary sinus floor and vertical facial skeletal patterns is important for designing orthodontic treatment plans. We correlated the extension of the maxillary sinus (MS) floor with different facial skeletal malocclusion in adolescent patients aged 10-19 years old using a cone-beam computed tomography. Methods: The relationship between the root tips of upper posterior teeth and the sinus floor was typed and scored (0-4) using cone-beam computed tomography (CBCT) images. Scores of each tooth and each patient were formulated.The cephalometric radiographs were analyzed with Dolphin software to diagnose patients' facial skeletal types into three groups according to Frankfort mandibular plane angle (FMA) as high-angle, average-angle and low-angle groups and ANB angle as Class I, Class II and Class III groups separately. The influences caused by age, sex, and facial skeletal malocclusion on the tooth and patient score were analyzed. Results: In high-angle group, the first molar (FM) score was significantly higher than that in the average-angle and low-angle groups (P = 0.018). Age has a positive effect on the patient score and some of the tooth scores, such as the second premolar (SPM) score, FM score, and the second molar (SM) score, and in the skeletal facial malocclusion. With increasing age, SM score increased along with the Frankfort mandibular plane angle (FMA). No significant difference was found in the distribution of patient and tooth scores by ANB angles. Conclusion: The relationship between the maxillary posterior roots and the sinus floor is correlated with facial skeletal malocclusion in 10- to 19-year-old adolescents. More first molar root tips were inside the sinus in the high-angle group compared with the average-angle and low-angle skeletal patterns. With advancing age, more second molar root tips were more close to contact the sinus floor in the high-angle group. Consideration of the root-sinus position in the posterior maxillary area before establishing an orthodontic treatment plan is recommended.