The molecules released from cells undergoing necrosis are recognized as alarmins, and S100A8/9, a typical alarmin, is associated with several inflammation-related diseases. This study was to investigate the molecular role of S100A8/A9 on the process of intervertebral disc degeneration (IVDD) and inflammation-related pain. The expression pattern of S100A8/A9 in different degenerated human nucleus pulposus (NP) tissues were measured by Real-time quantitative reverse transcription PCR (RT-qPCR) and immunohistochemical (IHC). The effects of S100A8/A9 on matrix production were assessed by RT-qPCR, western blotting, and cell immunofluorescence. Involvement of TLR4 and NF-κB signaling pathways were studied by pharmachemical inhibitors and small interfering RNAs (siRNAs). The development of degenerative and pain features in the IVDD model were examed by IHC and pain-behavior testing. The expression of S100A8/A9 was significantly elevated in severely degenerated human NP tissue with similar expression pattern of TNF-α. In NP cells, S100A8/A9 increased MMP-3/13, TNF-α, IL-6 expression and inhibited aggrecan and collagen II expression. RT-qPCR and western blotting showed that the regulatory effects of S100A8/A9 on IVD were TLR4 dependent. Pharmacological inhibition or siRNA knockdown of the NF-κB signaling attenuated S100A8/A9-induced upregulation of MMP-3/13, TNF-α and IL-6. In vivo, S100A9 inhibitor treatment inhibited disc-puncture induced IVDD and inflammation-related pain. This study showed that S100A8/A9 bound to TLR4 and increased the expression of MMPs, TNF-α, and IL-6 through NF-κB signaling pathways in NP cells. Furthermore, S100A8/A9 inhibitor could prevent development of IVDD and inflammation-related pain in the rat model.