This study investigated the immunomodulatory effects of calcium phosphate (CaP) microspheres, focusing on how particle size influenced macrophage polarization and cytokine secretion patterns. SEM analysis revealed that HA microspheres predominantly exhibited a spherical shape with distinct sizes and sub-micro-sized pores. The average particle sizes for the S1, S2, and S3 groups were 17.36 μm, 27.59 μm, and 47.14 μm, respectively. In vitro experiments demonstrated that small-sized S1 microspheres were more readily phagocytosed by macrophages, leading to a pro-inflammatory M1 phenotype characterized by increased gene expression of iNos and inflammatory cytokines (IL-1β, IL-6, TNF-α), and a higher proportion of CCR7+ M1 macrophages. In contrast, the larger S2 and S3 microspheres favored an anti-inflammatory M2 phenotype, with higher expression of Arg and anti-inflammatory cytokines (IL-10), and greater proportions of CD206+ M2 macrophages. Additionally, HA microspheres were injected into mouse quadriceps muscles, revealing significant differences in immune cell infiltration and tissue response. The S1 microspheres induced a prolonged and more severe inflammatory response, while the S2 and S3 microspheres were embedded in cell-rich tissue with minimal inflammation or fibrosis. It indicated the potential of larger microspheres (S2 and S3) to create a more favorable immune microenvironment that supported faster and more effective tissue healing. These findings underscore the importance of optimizing microsphere size to achieve desired immunomodulatory effects, thereby enhancing their clinical efficacy.