Porcine Reproductive and Respiratory Syndrome (PRRS) is an acute, highly contagious swine infectious disease caused by the PRRS virus (PRRSV). Due to the frequent mutation and recombination of PRRSV, the current commercial vaccines cannot provide effective protection, and there is an urgent need to develop antiviral drugs. This study aimed to prepare a kind of zinc oxide−selenium nanoparticle (ZnO−Se NPs) and investigate their inhibitory effect on PRRSV proliferation. The hybridization of ZnO and selenium resulted in the synthesis of ZnO−Se NPs, which were then examined by using dynamic laser light scattering and transmission electron microscopy for characterization. The ZnO−Se NPs showed excellent stability and dispersibility, measuring an average diameter of 90 nm. MTT assay revealed that ZnO−Se NPs had good biocompatibility and low toxicity below 2.5 μg/mL. Various experiments have shown that ZnO−Se NPs have the ability to effectively suppress the proliferation of PRRSV in a dose-dependent fashion. Moreover, this inhibition was equally effective against other subgenotypes of PRRSV and non-RNA viruses, indicating that ZnO−Se NPs had broad-spectrum antimicrobial properties. Mechanism investigations revealed that ZnO−Se NPs inhibited PRRSV primarily by targeting the replication process through upregulation of the expression of NLRX1, a protein that interacts with PRRSV Nsp9, and by inhibiting PRRSV-induced upregulation of ROS, rather than by stimulating the innate immunity. This work emphasized the antiviral impact of ZnO−Se NPs and offered compelling evidence of their potential as a promising therapy against PRRSV and other viral infections.