Abstract Background Understanding the anatomical relationship between the maxillary sinus floor (MSF) and the posterior maxillary teeth (PMT) is important when planning the orthodontic intrusion of the posterior teeth. This study aimed to determine the vertical relationship between posterior maxillary teeth and maxillary sinus floor in different skeletal classes in the Chinese adult population. Methods This is a retrospective cross-sectional study involved cone beam computed tomography images of 298 adult patients (145 males and 153 females) between 20 and 45 years old. The sample was categorized according to A point, Nasion, B point (ANB) angle into 102 Class I, 102 Class II, and 94 Class III malocclusion. Non-parametric Wilcoxon Mann–Whitney U and Kruskal–Wallis tests were used to compare the studied groups. The Intra-class Correlation Coefficient (ICC) was used to assess the intra- and inter-observer reliability analysis. Results Overall, there was a statistically significant difference in the mean distance between both genders (P