Abnormally expressed miR-218-5p involves in alveolar bone defect. We intend to investigate whether miR-218-5p-modified bone marrow mesenchymal stem cells (BMSCs) mediates the healing effects of EphrinB2-EphB4 signals on the alveolar bone defect. Fifty germ-free rats (6-month-old) were utilized in this study. The grouping was set up as follows: blank group, model group, miR-218-5p group, EphrinB2-EphB4 antagonist group, and positive control group (10 rats in each group). HE staining was employed to quantify bone resorption lacunae number. And the following indicators were monitored: miR-218-5p expression, differentiation status of osteoblasts, concentrations of TNF-α/IL-10/ IL-8, and EphrinB2 and EphB4 expression. As shown in HE staining, massive infiltration of inflammatory cells was denoted at the alveolar bone defective sites in rats from model group. However, infiltration of inflammatory cells in lesions was moderate in rats from EphrinB2-EphB4 antagonist group and positive control group, which was accompanied by formation of small bone islands. Furthermore, lesser infiltration of inflammatory cells was denoted at the alveolar bone defective sites in rats from the miR-218-5p group, which also exhibited a larger number of newly formed bone trabeculae growing toward the center of lesions. On the 3rd day of culture, absorption lacunae were rare in the model group, while remaining undetectable in other groups. On the 7th day of culture, bone resorption lacunae number in samples from model group was significantly higher in comparison with that in other groups. Meanwhile, it was reduced significantly in miR-218-5p group. However, it was increased in EphrinB2-EphB4 antagonist group and positive control group (P <0.05). An elevation of the intracellular miR-218-5p level was denoted in the modified BMSCs in comparison with those unmodified BMSCs (P < 0.05). In comparison with blank group, other groups exhibited significantly elevated ALP levels, among which model group showed highest level. However, decline of ALP levels was denoted in positive control group, EphrinB2-EphB4 antagonist group and miR-218-5p group, with lowest ALP level in miR-218-5p group (P <0.05). Except blank group, rats in other groups exhibited a significant elevation of TNF-α, IL-10 and IL-8 in the serum, among which those in the model group displayed the most remarkable increase of these cytokines. Rats in miR-218-5p group, EphrinB2-EphB4 antagonist group and positive control group exhibited significantly reduced levels of IL-8, IL-10 and TNF-α in the serum, with miR-218-5p group showing lowest levels (P < 0.05). In comparison with the blank group, other groups showed significantly enhanced protein expression of EphrinB2 and EphB4, among which the model group displayed the most remarkable enrichment of these proteins. In comparison with the model group, samples from the miR-218-5p group, EphrinB2-EphB4 antagonist group and positive control group exhibited significantly weakened expression of EphrinB2 and EphB4, among which the miR-218-5p group displayed the most remarkable decrease of these proteins (P <0.05). miR-218-5p-modified BMSCs can modulate the EphrinB2-EphB4 signal transduction pathway to produce two-way transmission, which included their inhibition of the osteoclast generation and their enhancement of the osteoclast differentiation. In this way, they aided in alleviating inflammatory response in alveolar bone defective lesions, thereby accelerating the healing process of alveolar bone defect. The function of miR-218-5p-modified BMSCs is mainly achieved in the healing process of the alveolar bone defect.