Objective To investigate the early and mid-term clinical outcomes of the modified cone reconstruction in the treatment of Ebstein’s anomaly (EA). Methods Clinical data of 18 consecutive patients with EA in our hospital between May 2008 and August 2015 were retrospectively analyzed. All patients were diagnosed by echocardiography. There were 8 males and 10 females with an average age of 20.3 years ranging from 5 to 41 years. According to New York Heart Association classification, 12 patients were classified into grade Ⅱ and 6 grade Ⅲ. One patient had acute arterial embolism and amputation of left lower extremity caused by paradoxical embolism of combined secundum atrial septal defect, and another one was combined with double-orifice technique due to postoperative poor closure of tricuspid valve. The modified cone reconstruction was used to correct the EA, to make leaflets coapted well and form central blood flow. For those patients whose anterior leaflet developed poor and smaller, valve leaflet was widened by using autologous pericardial. For all patients, tricuspid annulus was reinforced by autologous pericardial. Results Two patients suffered arrhythmia, and returned to normal after medication. The rest patients recovered well without death. Echocardiography found 1 patient with moderate regurgitation and the rest of patients’ leaflets coapted well and had no tricuspid stenosis. They were followed up 9 to 38 months postoperatively, and cardiac function of gradeⅠin 14 patients and gradeⅡin 4 patients. Conclusion The early and mid-term clinical outcomes of the modified cone reconstruction in the treatment of EA are affirmative which can make leaflets coapt completely and have a strong anti-regurgitation ability, reducing the incidence of re-operation, valve replacement and postoperative mortality.