This study aimed to determine the effectiveness of different aligner anchorage preparations on mandibular first molars during premolar-extraction space closure with clear aligners and to assess the effects of different modes of Class II elastics on mandibular first molars. Finite element models were constructed on the basis of cone-beam computed tomography data from an orthodontic patient. The models comprised maxilla, mandible, maxillary and mandibular teeth without first premolars, periodontal ligaments, attachments and aligners. Tooth displacement tendencies were calculated using different aligner anchorage preparations and Class II elastics on the models from the same patient. Three group sets were designed on the basis of the positions of aligner cutouts and buttons (mesiobuccal, distobuccal and lingual). Four groups were established in each of the 3 group sets. Four groups were created: (1) no elastic traction+ no anchorage preparation, (2) anchorage preparation only, (3) elastic traction only, and (4) elastic traction+ anchorage preparation. Different aligner anchorage preparations (0°, 1°, 2°, 3°) were applied on mandibular second premolars and molars. The Class II traction force was set to 100 g. With clear aligners, mandibular first molars were subject to mesial tipping, lingual tipping and intrusion. In the condition of no elastic traction, aligner anchorage preparation resulted in distal tipping, buccal tipping, and extrusion effect on mandibular first molars. Aligner anchorage preparation was more effective in the distal and lingual cutout groups than in the mesial cutout group. In the condition of Class II elastic traction, the bodily movement of mandibular first molars was achieved with a 3° anchorage preparation for the mesial cutout group and a 1.7° anchorage preparation for distal and lingual cutout groups. Absolute maximal anchorage was achieved with a 2° anchorage preparation for distal and lingual cutout groups. Clear aligner therapy caused mesial tipping, lingual tipping and intrusion of mandibular first molars during premolar-extraction space closure. Aligner anchorage preparation effectively prevented mesial and lingual tipping of mandibular molars. Distal and lingual cutout modes were more effective than mesial cutout modes in aligner anchorage preparation. For each aligner stage (0.25 mm), 1.7° aligner anchorage preparation and Class II elastics with distal or lingual cutouts led to the bodily movement of mandibular first molars, whereas 2° anchorage preparation reached absolute maximal anchorage.