We obtained the global proteomic and ubiquitylomic data of epididymal VAT from lean and obese male mice by mass spectrometry. Our proteomic analyses revealed significant changes of metabolic pathways involved in fatty acid, acyl-CoA and branched chain amino acids metabolism in obese VAT. Intriguingly, our integrated analysis of proteomic and ubiquitylomic data highlighted a discordance in the quantity changes of certain proteins and their ubiquitination levels. Notably, STEAP4 exhibited a markedly reduced protein level coupled with an enhanced K48-linked ubiquitination, suggesting a potential role for ubiquitination-mediated proteasome degradation in VAT dysfunction. Collectively, this study introduces the first combined proteomic and ubiquitylomic examination of murine VAT, offering novel insights and potential therapeutic targets for obesity.