Mesenchymal stem cells (MSCs) and their secreted molecules have shown great potential for tissue regeneration and the treatment of inflammation and autoimmune diseases. However, they can also be associated with therapeutic failure or even side effects. Possible causes for this could include the state of the stem cells themselves and the influence of the local microenvironment, wherein macrophages play important roles. As such, we utilized conditioned medium from bone marrow-derived MSCs (MSC-CM) and studied its effect on different macrophage subsets. Effects on macrophage proliferation, apoptosis, polarization, and phagocytosis were determined, and it was discovered that MSC-CM had no significant effect on macrophage proliferation but inhibited M0 macrophage apoptosis and marginally induced M1 macrophage apoptosis. MSC-CM was shown to reduce CD80 expression on the surface of M1 macrophages. Moreover, it promoted and inhibited CD163 expression on the surface of M0 and M1 macrophages, respectively. However, MSC-CM tended to initially promote CD163 expression on M2 macrophages but inhibited expression of this marker after additional incubation time. Unlike MSCs, MSC-CM had no significant effect on the expression of TNF-α and IL-10 in macrophages. Thus, the effect of MSC-CM on different types of macrophages is different, and after stem cells are implanted, their effects on the local immune microenvironment are closely related to the original immune status of the implantation site. Therefore, we suggest that when utilizing stem cells for therapeutics, the immune status of the treatment site should be fully elucidated.