Gastrointestinal stromal tumor (GIST) is an uncommon mesenchymal tumor of the gastrointestinal tract and is generally located in the stomach and small intestine. They usually present with abdominal pain, gastrointestinal bleeding, and palpable mass. Some patients present with rare symptoms that are more common in malignant GIST. Malignant GIST combined with a liver abscess has not been reported yet in the literatures. We report a case of 67-year-old woman who suffered from liver abscess combined by malignant GIST with central necrosis and fistula in the ileum. She complained of fever, chills, and abdominal pain. Abdominal CT scan showed huge liver abscess and ileal mass with air pocket. Small bowel series showed contrast material filling into the ileal GIST mass. An operation was performed and the final diagnosis was malignant GIST of the ileum with invasion into the sigmoid colon and urinary bladder.