Objective To analyze the common post-operative complications of microwave ablation in situ in the treatment of bone tumors and the prevention and control strategies. Methods Between March 2009 and July 2012, 73 cases of bone tumors were treated with microwave ablation in situ, of which 54 cases met the inclusion criteria. There were 31 males and 23 females with a median age of 27 years (range, 9-74 years), including 37 malignant tumors and 17 benign tumors. In 49 primary bone tumors, 17 cases were in stage 3, 13 in stage IIA, and 19 in stage IIB according to Enneking grading system. The postoperative complications, managements, and outcomes in patients were analyzed. Results After operation, 54 patients were followed up 12-40 months (mean, 24 months). Seven kinds of complications occurred in 21 patients (38.9%) with 3 cases suffered from more than one, including pathologic fracture in 4 cases (7.4%), deep infection in 2 cases (3.7%), nerve injury in 7 cases (13.0%), deep vein thrombosis of the lower extremity in 1 case (1.9%), medial collateral ligament heat injury of the knee in 1 case (1.9%), hematoma in 2 cases (3.7%), and fat liquefaction of incision and flap necrosis in 8 cases (14.8%). Conclusion Pathologic fracture is the primary complication which results in a second surgery. Deep infection is the main complication that often leads to failure of the limb salvage. Nerve injury and poor wound healing are the most common complications. Good control of microwave temperature is the key to successful operation, and the related preventive strategies could reduce complications.