Porcine reproductive and respiratory syndrome (PRRS), caused by porcine reproductive and respiratory syndrome virus (PRRSV), is an acute infectious disease. The prevalence of PRRS has made swine industry suffered huge financial losses. Matrine, a natural compound, has been demonstrated to possess anti PRRSV activity in Marc-145 cells. However, the underlying molecular mechanisms were still unknown. The main objective of our study was to discuss the effect of Matrine on PRRSV N protein expression and PRRSV induced apoptosis. Indirect immunofluorescence assay (IFA) and Western blot were used to assess the effect of Matrine on N protein expression. Apoptosis was analyzed by fluorescence staining. In addition, the effect of Matrine on caspase-3 activation was investigated by Western blot. Indirect immunofluorescence assay and Western blot analysis demonstrated that Matrine could inhibit N protein expression in Marc-145 cells. And Matrine was found to be able to impair PRRSV-induced apoptosis by inhibiting caspase-3 activation.