Aim: The aim of the present study was to analyze the morphological variations and complexities in root canal systems of the maxillary second molars in South Indian population, using cone beam computed tomography (CBCT). Subjects and Methods: The CBCT images of 500 participants were examined at different slice thickness of 125 micrometers. Root canal systems of the 500 maxillary second molars were analyzed according to Vertucci, HMA Ahmed et al., and Kim et al. classifications in the Indian subpopulation. Statistical Analysis Used: Interobserver variability was analyzed using Kappa statistics. Results: Among the tooth analyzed, 63% had three roots, with a single canal in each root in 65.2% tooth. About 41.8% of the tooth had fusion of mesiobuccal and distobuccal roots. The most commonly found root canal configuration was Type I (65%) according to Vertucci's classification. According to HMA Ahmed et al. classification, 67.9% tooth had the configuration of 327 MB1 DB1 P1/317 MB1 DB1 P1. Nearly 20.8% tooth had MB2 canal. The most common isthmus type was Type II (55.2%) according to Kim's classification, and the prevalence of isthmus was 2–5 mm from the root apex. Conclusions: The number of roots, canals, their configuration, and occurrence of isthmus has not been reported in the South Indian population. The importance of understanding the knowledge of the anatomy of teeth during the treatment of maxillary second molars would contribute to successful endodontic outcomes.