Chondrosarcoma is the most common primary malignant bone tumor of the hand, Mesenchymal chondrosarcoma (MCS) is a rare subtype of chondrosarcoma, extraosseous mesenchymal chondrosarcoma (EMCS) is even rarer. METHODS We presented a case of primary EMCS involving the distal thumb in a 59-year-old man. The patient had abnormally grown nails and a higher skin temperature than the contralateral finger. After admission to our hospital, we found that the tumor has the possibility of malignant transformation, but imageological examinations did not reveal invasive bone lesions and calcification. Finally, due to the patient's strong desire to preserve the thumb, a conservative surgical approach was selected to preserve the patient's finger function, and histological examination indicated MCS. CONCLUSIONS EMCS is a highly malignant tumor with strong tendency of invasion and metastasis. Imaging is sometimes difficult to diagnose, and pathology is a necessary part of distinguishing between benign and malignant tumors. Operation is the major treatment to EMCS, meanwhile, adjuvant radiotherapy and chemotherapy also be effective. The overall prognosis is poor.