Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology capable of analyzing host and viral transcripts and host–virus interactions at the single-cell level. Viral infection is a complex process involving interactions between the virus and the host cell. While traditional research methods often have difficulty revealing cellular heterogeneity and dynamics during viral infections, scRNA-seq technology, which enables the sequencing of individual cells, provides a powerful tool for the in-depth study of viral–host interactions. scRNA-seq was able to reveal the mechanism of molecular changes in host cells during viral infection, providing new ideas and methods for the diagnosis and treatment of viral infections. This article describes the application, advantages, and experimental procedures of scRNA-seq in host virology.