Soil viruses act as invisible regulators in ecosystems, profoundly influencing virus-host interactions and soil health by encoding diverse auxiliary metabolic genes. Through processes such as lysing host bacteria to release nutrients, facilitating the transfer of functional genes, and regulating microbial community metabolism, they serve as critical drivers of functional succession and maintenance in soil ecosystems. This review systematically summarizes the roles of soil viruses in nutrient compensation and element cycling (e.g., carbon fixation, nitrogen fixation, sulfur cycling, and phosphorus metabolism), ecological environment improvement (e.g., pH regulation and saline-alkali land remediation), pollutant degradation, plant health promotion, control of antibiotic-resistant bacteria, and modulation of human health. Furthermore, the paper highlights limitations in current research, such as the lack of in-depth functional analysis methods and insufficient coverage of diverse habitats. Future studies should focus on exploring viral genetic resources and their safe engineered applications to provide innovative solutions for sustainable agriculture and pollution remediation.