Gastrointestinal stromal tumor (GIST), the most common mesenchymal neoplasm of the digestive tract, relies heavily on imaging for clinical diagnosis and management. Spectral CT transcends the limitations of conventional CT through multi-energy imaging technologies, with core techniques—including virtual non-contrast (VNC) imaging, monoenergetic imaging, material decomposition, effective atomic number analysis, and spectral curve analysis—enable quantitative assessment of tumor vascularity, composition, and metabolic characteristics. This advancement provides novel insights into the diagnosis, genotype prediction, treatment response evaluation, and prognosis prediction of GIST. This review systematically examines the clinical utility of spectral CT in GIST, highlighting the distinctive advantages of iodine concentration, spectral curves, and VNC-derived parameters in characterizing tumor features. Additionally, limitations and future research directions are discussed.