Noncoding RNAs (ncRNAs) are key components of the transcriptome and play an important role in both normal biological activity and pathological processes such as viral infection and tumorigenesis. LncRNAs and miRNAs are the most important elements of ncRNAs and function as vital regulatory elements. Their complex regulatory relationship has therefore attracted a lot of attention. In this review, we address the generation, classification, and regulatory mechanisms of lncRNAs and miRNAs in the interaction between virus and host, focusing on their mutual regulation in viral replication and pathogenesis. In-depth analysis of the underlying mechanisms will provide new information for the prevention of viral infections and development of antiviral drugs.