Intra-abdominal desmoid tumor (IADT) and gastrointestinal stromal tumor (GIST) are both mesenchymal tumors mostly found in gastrointestinal tracts and easily misdiagnosed, which would directly damage the survival prognosis and quality of life of patients. With the advent of the era of precision medicine, the understanding of the above two diseases is more in-depth, and the requirements for accurate diagnosis and individualized precision treatment are more stringent. Moreover, there seems to be some internal relationship between IADT and GIST, and the lack of systematic research and discussion makes clinical decision-making and patient management easy to fall into traps and misunderstandings. Therefore, this paper reviews the clinical characteristics, pathogenesis and treatments of the two, and explore their differences and internal relations, so as to provide research and practical reference for promoting more precise and individualized diagnosis and treatment regimens.