Objective: This study aimed to observe and quantify the continuous changes in dental movement and trabecular microstructure in tension and pressure zones of rats under orthodontic force using in vivo Micro-CT scanning. Methods: A 50g orthodontic force was applied to the left maxillary first molar of five male 8-week-old SD rats. The rats were scanned in vivo at different time points using Micro-CT. The distance of orthodontic tooth movement was calculated in a unified spatial coordinate system. Additionally, trabecular micro-morphological and mechanical property-related parameters in the tension and pressure zones of the moved teeth were measured and statistically analyzed. Results: There was significant displacement of the rat molars within the first 0-3 days, with a decrease in movement rate between 3-14 days, followed by an increase in rate from 21-28 days (P<0.001). Multiple trabecular parameters in both tension and pressure zones showed turning points at 7 days and 14 days, respectively. Specifically, bone volume fraction (BV/TV) and trabecular thickness (Tb. Th) first decreased and then increased, while total porosity volume [Po. V(tot)], structure model index (SMI), trabecular separation (Tb. Sp), and fractal dimension (FD) exhibited the opposite trend. During the early stage of tooth movement, the slope of increase in trabecular parameters was greater in the tension zone compared to the pressure zone. In the later stage of tooth movement, there were significant differences in the values of BV/TV, Po. V(tot), SMI, and Tb. Sp between the tension and pressure zones (P<0.05). Conclusion: Orthodontic tooth movement in rats occurs in three stages. There are differences in trabecular microstructure remodeling between tension and pressure zones, with bone mass and bone quality both decreasing first and then increasing, reaching their lowest points around 7 days and 14 days, respectively. The active phase of bone resorption in the tension zone occurs earlier, and bone formation in the alveolar bone of the tension zone lags behind bone resorption in the pressure zone.