This study sought to explore the role and significance of multidisciplinary team (MDT) discussion and comprehensive treatment in the diagnosis and treatment of a gastrointestinal stromal tumor (GIST) with liver metastasis. For GIST patients with liver metastasis, MDT can evaluate whether the liver metastasis is resectable, so as to formulate accurate treatment goals and the best diagnosis and treatment plan.A 53-year-old male patient with localized rectal GIST with metachronous liver metastasis (MLM) was admitted to Yunnan Cancer Hospital in October 2014. At the 1st visit, he was diagnosed with locally advanced rectal GIST, and a MDT discussion was held by departments of colorectal surgery, imaging, pathology and oncology. The tumor shrank after neoadjuvant targeted treatment with imatinib. A local resection of the rectal GIST was successfully performed via the anal approach. R0 resection was achieved and the function of the anal sphincter was preserved. Following the operation, oral imatinib treatment was discontinued after 2 years. The patient developed isolated liver metastasis 6 months later. After the MDT discussion by departments of colorectal surgery, hepatobiliary surgery, imaging, pathology, and oncology, R0 resection of the liver metastasis was achieved. After the operation, sunitinib was administered for 4.5 years. The patient's overall survival (OS) has reached 7.5 years. No tumor recurrence or metastasis was found in the re-examinations. The follow-up is ongoing.Targeted therapy combined with surgery is the most suitable way to cure GIST patients with liver metastasis. More importantly, the multi-disciplinary management and the standardized diagnosis and treatment of GIST patients with liver metastasis through MDT discussion can improve the quality of life and prolong the survival of patients.2022 Journal of Gastrointestinal Oncology. All rights reserved.