Gastrointestinal stromal tumors (GIST) originate from gastrointestinal mesenchymal tissue, and most of them are secondary to KIT/PDGFRA gene mutations. This discovery has a landmark significance for the basic research and clinical diagnosis and treatment of GIST. Genetic testing is widely used in many fields, such as identifying pathological diagnosis of gastrointestinal stromal tumor (GIST), judging prognosis and guiding targeted drug therapy. In recent years, numerous studies have shown that liquid biopsy techniques, including circulating tumor DNA (ct DNA) detection, have shown extremely important clinical value and broad application prospect for the diagnosis and treatment of gastrointestinal stromal tumor (GIST). This article reviews the value of circulating tumor DNA (ctDNA) detection in the diagnosis and treatment of gastrointestinal stromal tumors (GIST).