The aim was to investigate changes between autophagy and apoptosis in alveolar bone mesenchymal stem cells (BMSCs) under orthodontic pressure and the effect on osteogenesis in BMSCs. Twenty-four beagle canine teeth were used as experimental models. The control group received no treatment, while in the experimental groups, the canines were moved distally with 150 g of orthodontic force for 7 days, 14 days and 28 days. Bone remodeling was detected by H&E staining, while autophagy and apoptosis in the alveolar bone were analyzed by immunohistochemistry. 3-MA and Z-VAD-FMK were used to modulate autophagy and apoptosis. Transmission electron microscopy and western blotting were used to analyze autophagy and apoptosis in BMSCs, while their osteogenesis was analyzed by ALP staining, alizarin red staining, and osteogenic gene analysis. Compared to the control group, we observed significant distal movement of the canines in each of the experimental groups, the distance moved as the loading time was extended. In the experimental groups, the alveolar bone on the pressure side was clearly absorbed. On the pressure side, teeth were positive for LC3 after loading for 7 days and 14 days, whereas teeth were positive for caspase-3 after loading for 14 days and 28 days. The number of autophagosomes and the conversion of LC3-II/LC3-I gradually decreased, nevertheless, the number of apoptotic bodies and the expression of caspase-3 increased gradually. ALP activity, mineralized nodule formation, and osteogenic gene expression in BMSCs gradually decreased. Finally, the down-regulation of autophagy inhibited osteogenesis in BMSCs, whereas the restriction of apoptosis led to adverse consequences. Collectively, these data indicate that autophagy of the alveolar bone and BMSCs under orthodontic pressure gradually decreased as the loading time was extended, in contrast, the extent of apoptosis gradually increased; the osteogenic differentiation of BMSCs was positively correlated with autophagy but negatively correlated with apoptosis.