Toll-like receptors (TLRs) are one of the most important receptors for innate immunity to recognize pathogens and regulate the signaling pathway. Several mechanisms have been discovered which involved in TLRs-mediated pathways in inflammatory and autoimmune diseases, however, the therapeutics of these are still under investigation. Here, we designed phage-displayed peptide library to screen the novel TLR4/MD2 binding peptides. Phage display has been proved to be a powerful technology to screen the proteins, cells or tissues binding specific peptides. After several rounds of biopanning, high throughput screening, ELISA assay was performed and the binding affinity of selected single phage particles with TLR4/MD2 complex were measured. The phage clones showing high binding affinity with TLR4/MD2 were isolated and sequenced. The synthesized peptides antagonized LPS-induced activation of nuclear factor (NF)-κB in TLR4/MD2/CD14-transfected human embryonic kidney (HEK)-293 cells. To confirm the LPS antagonistic effect of selected peptides, the NF-κB nuclear translocation, IL-6 and NO level were investigated in peptide treated Mouse macrophage cells (RAW264.7). Extensive computational strategies were further applied to explore the possible binding pattern of TLR4/MD2 and selected peptides. These findings suggest the therapeutic potential of screened peptides against TLR4/MD2 related immune diseases but further validation in inflammatory and immune related disorders is needed.