AIM: This study aimed to evaluate the anatomical differences in the alveolar bone at edentulous sites of the mandibular first and second molars using cone-beam computed tomography (CBCT) and to assess their impact on implant outcomes, thereby providing clinical insights to improve implant success in the mandibular second molar region. METHODS: A total of 504 patients with missing mandibular first or second molars were recruited in the Department of Stomatology at Foshan Fosun Chancheng Hospital between June 2020 and June 2023. These patients were divided into two groups: mandibular first molar loss (n = 226; as ‘first-molar group’) and mandibular second molar loss (n = 278; as ‘second-molar group’). All patients underwent CBCT imaging, and measurements for parameters such as alveolar bone inclination, alveolar ridge width, and the distance from the alveolar crest to the mandibular canal were taken. Postoperative evaluations were conducted to assess deviations in the implant neck, apex, and insertion angle and to analyze the effect of anatomical parameters on implant outcomes in the mandibular second molar region. RESULTS: There were no significant differences between the two groups in terms of sex, age, duration of tooth loss, presence of third molars, or smoking history (p > 0.05). The first-molar group exhibited significantly higher values for alveolar bone inclination, alveolar ridge width, and canal-crest distance compared to the second-molar group (p < 0.05). Immediately post-implantation, the neck deviation, apical deviation, and insertion angle deviation were all significantly lower in the first-molar group than in the second-molar group (p < 0.05). Six months postoperatively, the implant failure rate for the second-molar group (9.45%, p < 0.001) was significantly higher than that for the first-molar group (0.00%), along with greater marginal bone resorption (p < 0.001). Additionally, patients with failed implants in the mandibular second molar region showed significantly lower preoperative alveolar bone inclination than those with successful implants (p < 0.05). CONCLUSIONS: The second-molar group presents less favorable anatomical conditions, such as reduced canal-crest distance and increased alveolar bone inclination, which may contribute to greater implant deviation when placed freehand. These findings suggest a need for enhanced preoperative planning and surgical precision in this region. However, as these observations are based on CBCT measurements and not direct intraoperative evidence, further studies are needed to validate these findings. Lower alveolar bone inclination may be a key factor in implant failure, highlighting the critical importance of preoperative planning and surgical precision in mandibular second molar implant procedures.