Objective: This study aimed to evaluate the effects of force loading on root damage caused by contact with temporary anchorage devices (TADs) during orthodontic treatment and to examine the repair process 4, 8, and 12 weeks after TAD contact by micro-computed tomography (CT). Methods: We enrolled 42 volunteers who required bilateral upper first premolar extractions. The experimental study design was as follows. For both first premolars, cantilever springs were placed, and then TADs were immediately inserted between the premolars of all volunteers. According to the removal order of the appliances, the participants were divided into the TAD group (Group T: n = 21, only TAD removal) and the spring group (Group S: n = 21, only spring removal). A split-mouth design was adopted in both groups as follows. For each volunteer, the left premolars were extracted 4, 8, or 12 weeks after TAD-root contact. The right premolars were extracted immediately after contact in both groups (Groups T-C and S-C) and used as positive controls. Resorption volumes and numbers of craters were determined by micro-CT. Results: The numbers of resorption craters were higher in Group T than in Group S at 8 and 12 weeks (p < 0.01). Crater volumes were higher in Group T than in Group S at 4 and 12 weeks (p < 0.01, both). Conclusions: Root injury was not completely repaired 12 weeks after root-TAD contact, even when the TADs were removed in cases of continuous force application.