As a crucial kinase in the host antiviral innate immune signaling pathway, TANK-binding kinase 1 (TBK1) is strictly regulated by various posttranslational modifications. Previous studies have demonstrated that the stability of TBK1 can be compromised through autophagy; however, the precise mechanisms involved in the regulation of TBK1 degradation remain unclear. In this study, we revealed that the E3 ubiquitin ligase Stub1 can inhibit the production of type I interferon (IFN-I) by targeting TBK1, thereby preventing host antiviral responses. Mechanistically, TBK1 is targeted for degradation by chaperone-mediated autophagy (CMA), which depends on its three typical motifs. This process relies on the interaction between TBK1 and Stub1. Simultaneously, Stub1 catalyzes the polyubiquitination of TBK1 at lysine 344 (K344), which is linked to K27. The ubiquitinated TBK1 is recognized by heat shock cognate protein 70 (HSC70/HspA8), resulting in autophagic degradation via CMA mediated by LAMP2A. Compared with wild-type mice, Stub1-deficient mice exhibit increased resistance to VSV and HSV-1 infection, accompanied by increased expression levels of type I IFN. Overall, our findings reveal a TBK1-Stub1 axis in the RIG-I and cGAS-STING pathways, highlighting the effects of CMA on host antiviral innate immune responses.