Background <p>Maxillary molars have a wide range of anatomical variations. The presence of atypical root canal structures, such as the second mesiobuccal (MB2) canal, complicates endodontic procedures. The purpose of this study was to analyze the differences in root and canal morphology of the maxillary first and second molars in a Chinese Kazakh population by using cone-beam computed tomography (CBCT).</p> Methods <p>The study included 407 patients, examining maxillary first molars (<i>n</i> = 669) and maxillary second molars (<i>n</i> = 693). The number of roots and canals was recorded, and canal configurations were classified using Vertucci’s system. The images were independently assessed by two endodontists, with any discrepancies resolved by a professional oral radiologist to achieve consensus. A chi-square test was used to assess the association between MB2 morphologies and demographic variables, including sex, age, and tooth position.</p> Results <p>Maxillary first and second molars typically exhibited three roots, with MB2 present in 56.0% and 24.3% of cases, respectively. The predominant MB2 canal type was Vertucci type IV, observed in 71.7% and 60.5% of cases, respectively. Among maxillary first molars, age (<i>p</i> = 0.001) and gender (<i>p</i> = 0.038) showed significant differences, while tooth position (<i>p</i> = 0.104) did not. Among maxillary second molars, age (<i>p</i> = 0.822), gender (<i>p</i> = 0.073), and tooth position (<i>p</i> = 0.392) did not show significant differences.</p> Conclusions <p>This study was the first to examine the occurrence of the MB2 canal in a Chinese Kazakh group. Under the limitations of the study, maxillary first molars showed a higher occurrence of MB2 than maxillary second molars.</p>