Graft-versus-host disease (GVHD) remains the least curable complication after allogeneic bone marrow transplantation (BMT). Myeloid differentiation factor 88 (MyD88) is an adaptor molecule critically involved in the toll-like receptor (TLR) signaling pathway. The Toll/IL-1 receptor (TIR) domains of MyD88 and TLR are interactional modules responsible for sorting and signaling via direct or indirect TIR-TIR interactions, which can contribute to all phases of GVHD progression. Here, we describe the mechanisms of the novel MyD88 inhibitor, TJ-M2010-5, and the discovery of its immunosuppressive properties in the context of GVHD and the graft-versus-tumor (GVT) effect in a fully MHC-mismatched murine model. TJ-M2010-5 potentially interrupted the conformation of the TIR domain through its predicted DD loops, BB loops, and Poc site, and inhibited the homodimerization of MyD88, the LPS-stimulated activation of dendritic cells, and the priming of donor allogeneic T cell proliferation in a dose-dependent manner. Oral administration of TJ-M2010-5 ameliorated the inflammatory environment, decreased the number of apoptotic cells, increased tissue repair in GVHD target organs, and suppressed lethal GVHD. Further, protection against GVHD by TJ-M2010-5 did not abrogate a GVT effect against SP2/0, a myeloma cell line. Our data define the mechanisms of actions and provide novel insight into the potential clinical uses of TJ-M2010-5 for GVHD prevention.