Due to the increase in the number of obese individuals, the incidence of obesity-related complications such as cardiovascular disease and type 2 diabetes is higher. The aim of the present study was to explore the effects of silybin on protein expression in obese mice. Firstly, serum was collected, and it was used to detect serum lipids and other serological indicators. Secondly, total protein from epididymal adipose tissue was extracted for differential expression analysis by quantitative tandem mass tag (TMT) combined with liquid chromatography-tandem mass spectrometry (LC–MS/MS), followed by bioinformatics and protein–protein interaction (PPI) network analyses of these proteins. Lastly, real-time polymerase chain reaction (RT-PCR) and parallel reaction monitoring (PRM) were used to further validate the expression of identified differentially expressed proteins (DEPs) at the mRNA and protein level, respectively. The results revealed that silybin could improve abnormal lipid metabolism caused by the high fat diet in obese mice. A total of 341, 538 and 243 DEPs were found in the high fat/control (WF/WC), silybin/high fat (WS/WF) and WS/WC groups, respectively. These DEPs mainly participated in lipid metabolism and energy metabolism. Notably, tropomyosin 1 (TPM1), myosin light chain 2 (MYL2), myosin heavy chain 11 (MYH11) and other DEPs were involved in hypertrophic cardiomyopathy, dilated cardiomyopathy and other pathways. Silybin could protect cardiac function by inducing the protein expression of TPM1, MYL2 and MYH11 in the adipose tissue of obese mice.