The special organelle-located MAVS, STING and TLR3 are important for clearing viral infections. Although TLR4 triggers NF-κB activation to produce proinflammatory cytokines for bacteria clearance, effectors with special organelle localisation have not been identified. Here, we screened over 280 E3 ubiquitin ligases and discovered that the endoplasmic reticulum-located Hrd1 regulated TLR4-induced inflammation during bacterial infection. Hrd1 directly interacted with the deubiquitinating enzyme (DUB) Usp15. Unlike the classical function of Hrd1 in ER-associated degradation, Usp15 was not degraded but lost its DUB activity for IκBα deubiquitination, resulting in excessive NF-κB activation. Importantly, Hrd1 deficiency in macrophages protected mice against LPS-induced septic shock, and knock-down of Usp15 in Hrd1 KO macrophages restored the reduced IL-6 production. This study has proposed the crosstalk between Hrd1 and TLR4 linking the ER-plasma membrane function during bacterial infection.