Sepsis is a common clinical critical disease with high mortality. The excessive release of cytokines from macrophages is the main cause of out-of-control immune response in sepsis. Mesenchymal stem cells (MSCs) are thought to be useful in adjunctive therapy of sepsis and related diseases, due to their function in immune regulation, anti-inflammatory, antibacterial, and tissue regeneration. Also there have been several successful cases in clinical treatment. Some previous studies have shown that MSCs regulate the function of macrophages through secreting cytokines and extracellular vesicles, or transferring mitochondria directly to target cells, which affects the progress of sepsis. Here, we review the regulation of MSCs on macrophages in sepsis, mainly focus on the regulation ways. We hope that will help to understand the immunological mechanism and also provide some clues for the clinical application of MSCs in the biotherapy of sepsis.