Identifying viral-host interactions is central in understanding the pathogenesis of intracellular agents, such as bovine viral diarrhea viruses (BVDVs). A high expression level of BVDV NS3 protein is associated with its cytopathic (CP) biotype and is essential in viral replication and viral-induced apoptosis. Although the differences between CP and non-cytopathic BVDV biotypes are well established, especially the importance of the BVDV NS3 viral protein in giving rise to different biotypes, only a few studies identified BVDV-cellular partners. In this study, using a proteomics approach, we identified 71 bovine proteins that interact with the CP NS3 protein at three different time-points post-infection. Our results show that BVDV-host interaction dynamic network involves simultaneously and sequentially interacting proteins in different compartments of the host cells. System analysis of targeted proteins shows that CP BVDVs manipulate multiple and different pathways, primarily the ribosome/translation pathway, specifically at early stages of infection. At later stages of infection, when high levels of NS3 are present, apoptosis can be detected in infected cells. In addition, combining results from this study with previously identified protein interactions adds an extra dimension and higher connectivity to the BVDV strain NADL-host interaction network. Overall, our results indicate correlations among an increase in viral RNA translation, free NS3 level, and cytopathic effect associated with CP biotype infection. Finally, our approach highlights the dynamic interplay between BVDVs and host cells and identifies specific CP BVDV-host interactions that can be used as specific targets for further investigation as BVDV antiviral therapies.