Viral infectious diseases are highly diverse, with some viruses exhibiting high transmissibility or high variability, posing a persistent threat to global public health. Lipidomics, a crucial branch of metabolomics, provides unique insights into virus-host interaction mechanisms and facilitates the development of novel diagnostic and therapeutic approaches. This review systematically summarizes key applications of lipidomics in research on influenza viruses, severe acute respiratory syndrome coronavirus 2, human immunodeficiency virus, hepatitis viruses, and other viral pathogens. Studies demonstrate that these viruses exploit the host lipid metabolic network to facilitate entry, replication and immune evasion. Concurrently, dysregulation of lipid metabolites, such as eicosanoids, sphingolipids and lysophospholipids are closely associated with pathological processes including cytokine storms, tissue damage and disease progression. This review underscores the pivotal role of lipid metabolism in antiviral therapy and evaluates its translational potential, thereby offering innovative perspectives for the prevention and control of viral infectious diseases.