The mechanisms that enable Seneca Valley Virus (SVV) to escape the host innate immune response are not well known. Previous studies demonstrated that SVV 3C pro suppresses innate immune responses by cleavage of host proteins and degradation of IRF3 and IRF7 protein expression. Here, we showed that SVV 3C protease (3C pro ) has deubiquitinating activity. Overexpressed 3C pro inhibits the ubiquitination of cellular substrates, acting on both lysine-48-and lysine-63-linked polyubiquitin chains. SVV infection also possessed deubiquitinating activity. The ubiquitin-proteasome system was significantly involved in SVV replication. Furthermore, 3C pro inhibited the ubiquitination of retinoic acid-inducible gene I (RIG-I), TANK-binding kinase 1 (TBK1), and TNF receptor-associated factor 3 (TRAF3), thereby blocking the expression of interferon (IFN)-β and IFN stimulated gene 54 (ISG54) mRNAs. A detailed analysis revealed that mutations (H48A, C160A, or H48A/C160A) that ablate the Cys and His residues of 3C pro abrogated its deubiquitinating activity and the ability of 3C pro to block IFN-β induction.Together, our results demonstrate a novel mechanism developed by SVV 3C pro to promote viral replication, and may also provide a novel strategy for improving ubiquitination-based therapy.