To investigate the characteristics of spatial changes in molars and alveolar bone resorption among patients with loss of mandibular first molars. A total of 42 CBCT scans of patients with missing mandibular first molars (3 males, 33 females) and 42 CBCT scans of control subjects without loss of mandibular first molars (9 males, 27 females) were evaluated in this cross-sectional study. All images were standardized using the mandibular posterior tooth plane with Invivo software. The following indices regarding alveolar bone morphology were measured, including alveolar bone height, bone width, mesiodistal and buccolingual angulation of molars, overeruption of maxillary first molars, bone defects, and the capability of molar mesialization. The vertical alveolar bone height in the missing group was reduced by 1.42 ± 0.70 mm, 1.31 ± 0.68, and 1.46 ± 0.85 mm on the buccal, middle, and lingual side, respectively (no differences among the three sides; p > 0.05). Alveolar bone width was reduced the greatest at the buccal CEJ level and the least at the lingual apex level. Mandibular second molar mesial tipping (with mean of the mesiodistal angulation = 57.47 ± 10.34°) and lingual tipping (with mean of the buccolingual angulation = 71.75 ± 8.34°) were observed. The mesial and distal cusps of maxillary first molars were extruded by 1.37 mm and 0.85 mm, respectively. Buccal and lingual defects of alveolar bone occurred at the CEJ, mid-root, and apex levels. Through 3D simulation, the second molar cannot be successfully mesialized into the missing tooth position, and the difference between the available and required distances for mesialization was the greatest at the CEJ level. The duration of tooth loss was significantly correlated with the mesio-distal angulation (R = -0.726, p < 0.001), buccal-lingual angulation (R = -0.528, p < 0.001) and the extrusion of the maxillary first molar (R = -0.334, p < 0.05). Both vertical and horizontal resorption of alveolar bone occurred. Mandibular second molars exhibit mesial and lingual tipping. Lingual root torque and uprighting of the second molars are needed for the success of molar protraction. Bone augmentation is indicated for severely resorbed alveolar bone.