Upon invasion of host cells, viruses trigger a wide range of changes in the host genome, including alterations in chromatin conformation, gene expression regulation, DNA methylation, and histone modification. These genomic changes not only contribute to viral replication and latency but also may promote disease onset and progression by interfering with the host immune response. The profound impact of viral infection on the host genome has become an important area of current virology research. With the continuous advancements in genomics, 3D genome technology has become a powerful tool for revealing chromatin folding and interactions in three dimensions. In virology, 3D genomic technology can be used to determine how viruses regulate host gene expression by altering the conformation of the host chromatin, which in turn drives viral infections and related diseases. In recent years, Hi-C technology, a high-resolution 3D genome analysis method, has revealed how viruses integrate into host chromatin by capturing spatial contacts in three dimensions, providing insights into how these interactions affect the viral lifecycle, latent state, and host immune response. In a SARS-CoV-2 study, Hi-C technology revealed the interactions between the virus and specific regions of the host genome and elucidated how these interactions dynamically regulate the viral replication process and the modulation of the host immune response. By capturing spatial contacts at high resolution, Hi-C technology provides a unique molecular perspective for the study of viral infection mechanisms and promotes the further development of virology research. This chapter focuses on the basic principles of 3D genome technology and its application in virology, with a particular emphasis on the innovative use of Hi-C technology in the study of viruses such as SARS-CoV-2, especially its important contributions to understanding viral integration sites and chromatin recombination mechanisms. This chapter will also elaborate on the Hi-C experimental steps, required materials, and data analysis process, providing researchers with clear operational guidelines and assisting in the in-depth exploration of viral infection mechanisms.