Background: Periodontal disease is an inflammatory disease of periodontal tissues that is closely connected with systemic diseases. During periodontitis, the inappropriate recruitment and activation of monocytes–macrophages causes an increase in osteoclast activity and disrupts bone homeostasis. Therefore, it is a promising therapeutic strategy to treat periodontitis by regulating the functions of monocytes–macrophages. Litcubanine A (LA) is an isoquinoline alkaloid extracted from the traditional Chinese medicine Litsea cubeba, which was proven to have reproducible anti-inflammatory effects, but its regulatory role on bone homeostasis in periodontitis is still not clear. Methods: In this study, zebrafish experiments and a mouse ligature-induced periodontitis model were performed, and histological analysis was used to investigate the effect of LA on macrophage chemotaxis under the inflammatory environment. Real-time PCR was used to detect the regulatory effect of LA (100 nM ~ 100 μM) on the chemotaxis function of macrophages induced by LPS. Apoptosis assay and flow cytometry were used to elucidate the influence of LA on macrophage apoptosis and proliferation. To further clarify the regulatory role of LA on macrophage osteoclast differentiation, real-time PCR, histological analysis, western blot, and micro-computed tomography (micro-CT) were performed in vivo and in vitro to verify the impact of LA on bone homeostasis. Results: Compared with the control group, the chemotaxis function of macrophage was significantly attenuated by LA in vivo. LA could significantly inhibit the expression of genes encoding the chemokine receptors Ccr1 and Cxcr4, and its ligand chemokine Cxcl12 in macrophages, and suppresses the differentiation of osteoclastic precursors to osteoclasts through the MAPK signaling pathway. There were significantly lower osteoclast differentiation and bone loss in the LA group compared with the control in the ligature-induced periodontitis model. Conclusion: LA is a promising candidate for the treatment of periodontitis through its reproducible functions of inhibiting monocyte–macrophage chemotaxis and osteoclast differentiation. © 2023 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.