Understanding the anatomy of root canal systems and being aware of their variations is crucial for successful endodontic treatment. Specifically, the intricate and diverse nature of the root anatomy in maxillary third molars poses a significant challenge for dental clinicians. The study analyzed the morphology of the root canal system in maxillary third molars among residents of the Lower Silesia region in Poland using cone beam computed tomography (CBCT). This retrospective cross-sectional imaging study was conducted at the X-Ray Diagnostics Laboratory of the Academic Dental Polyclinic of Wroclaw Medical University, Poland. The study evaluated 316 CBCT scans and included 196 maxillary third molars. They were obtained from 118 females and 78 males over the age of 18, in the period from January to April 2022 (three consecutive months). The number of roots, root canals, and root canal configurations according to Vertucci's classification were analyzed. Three-rooted maxillary molars were found most often (64.29%), followed by single-rooted (24.49%), two-rooted (7.65%), and four-rooted (3.57%) teeth. Among all the roots examined, Vertucci Type I root canals were the most prevalent. Our research found that single-rooted forms (40 teeth, 33.89% vs. 8 teeth, 10.26%, p = 0.0013) of maxillary third molars were significantly more common in females than in males. However, three-rooted forms (62 teeth, 79.49% vs. 64 teeth, 54.24%, p = 0.0013) of maxillary third molars were significantly more common in males than in females. In the Lower Silesia region, the typical maxillary third molar in the Polish population has a three-rooted structure with Vertucci Type I root canal configuration. We noted a sex-dependent correlation in maxillary third molar morphology, with single-rooted forms more prevalent in women and three-rooted forms in men.