Gastrointestinal stromal tumors involving the rectum are rare, accounting for only 0.1% of rectal malignancy tumors, but the risk level is high with poor overall prognosis. Especially low rectal stromal tumors are rarer. Previous treatment is mainly surgery, the overall anal preservation rate is low, and easy to damage adjacent tissues and organs. One case report of a female patient with low rectal stromal tumors, after oral intake imatinib, anal tumor excision was performed, and oral intake imatinib was given after operation. No recurrence was found in the follow-up period of 7 months. For special location gastrointestinal stromal tumors that are unresectable or difficult to resect at the initial stage, and those operation may cause serious damage to the function of adjacent organs, it is expected to obtain the opportunity of operation and reduce the damage to organ function after preoperative treatment with imatinib.