BTG3, which belongs to the BTG/Tob gene family, is involved in various physiological processes. Infection with porcine epidemic diarrhea virus (PEDV), an alphacoronavirus, is associated with high mortality rates among piglets, contributing to major economic losses. This study elucidated a novel mechanism through which BTG3 suppresses PEDV replication. Endogenous BTG3 protein expression was upregulated in PEDV-infected host cells. PEDV replication was suppressed upon BTG3 overexpression but enhanced upon BTG3 knockdown. Additionally, BTG3 inhibited viral proliferation by targeting and degrading the S2 subunit of the PEDV spike (S) protein through both autophagy and proteasome pathways. BTG3 interacted and co-localized with the S2 protein, promoting S2 protein degradation through the recruitment of the cargo receptor NDP52 and the E3 ubiquitin ligase MARCHF8. In summary, this study elucidated a novel antiviral mechanism in which the host BTG3 targeted the viral S2 protein to inhibit PEDV proliferation through autophagy and proteasome pathways. These findings indicate that BTG3 is a potential novel target for the prevention and control of PEDV.