This study aimed to investigate whether the presence of two palatal roots on permanent maxillary second molars (MSMs) can affect the crown size and crown's buccolingual and mesiodistal diameters. A retrospective study was conducted using 592 CBCT scans to investigate 1120 MSMs of Mongoloid Malaysians. 3D models were created to assess the four-rooted MSMs and other related teeth carefully. Crown size and crown's buccolingual and mesiodistal diameters were measured for the four-rooted MSM, the adjacent maxillary first molar (MFM), and their antimeres to investigate the effect of the presence of an extra root on the size and morphological features of the crown of these associated teeth. Only six out of the 1120 MSMs displayed four roots (0.53%). The incidence was 0.67% (2/298) for the Malay males and 0.4% (1/247) for the Malay females, with the Malay male having a bilateral occurrence of four-rooted MSM. The incidence was 0.34% (1/294) for the Chinese males, while 0.71% (2/281) was detected in Chinese females. Interestingly, the four-rooted MSMs showed a wider mesiodistal distance than their three-rooted antimeres in three out of four cases. The presence of two palatal roots may also increase the crown's buccolingual diameter. The presence of anatomical variations and the dramatic change in crown measurements can be good indicators of the presence of extra roots, including in some of their related neighbours. This might help dentists to take precautionary measures when performing tooth extractions and endodontic therapy.