Viral myocarditis is a main cause of heart failure in young adults, which characterized by cardiac inflammation and caused by Coxsackievirus B3 (CVB3) infection. However, efficient therapies targeting inflammation and inflammatory response pathway are still elusive. Shenqi Fuzheng injection (SQFZI) is extensively applied in the cardiovascular diseases. But whether SQFZI may affect cardiac inflammation during acute viral myocarditis remains to be elucidated. The purpose of the present study was to investigate the potential protective effect of SQFZI on CVB3-induced myocarditis. Total of 120 mice were intraperitoneally inoculated with CVB3 to establish acute viral myocarditis model. For the CVB3-infected mice model, the body weight, mortality was observed. RT-PCR, western blot and immunohistochemistry methods were selected to detect the TRAF6 expression in myocardial tissues. We found that the expression of TRAF6 mRNA and protein were markedly and persistently increased during the progression of CVB3-induced myocarditis. The serum enzymes activity, including CK, CK-MB, LDH, AST, were also enhanced in CVB3-induced myocardial tissues. Notably, injection with SQFZI remarkably reduced CVB3-induced TRAF6 production and alleviated the severity of myocarditis. This study demonstrates the protective role of SQFZI against CVB3-induced myocarditis, which may explore a new therapeutic strategy for the treatment of viral myocarditis.