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