Objective To summarize the result and experience of modified Fontan procedure for patients with heterotaxy syndrome. Methods We retrospectively analyzed the clinical data of 17 patients with heterotaxy syndrome underwent cardiac operations in our hospital from September 2008 to November 2014. There were 11 males and 6 females at mean age of 4.7±2.5 years ranging from 3 to 10 years and at mean weight of 16.6±4.9 kilogram ranging from 10.6 to 27.0 kilogram. Two patients accepted modified Fontan surgery of stage one. The rest 15 patients accepted staging operation. They accepted modified Fontan surgery after they accepted a series of surgery like bidirectional Glenn procedure. Results There was no mortality in hospital. The peripheral blood oxygen saturation raised from 73%±12% to 91%±5%. There was no complications existing like thrombosis or severe arrhythmia. The follow-up duration was from 4 months to 6.5 years. There was 1 death during the time. The early and middle term mortality was 5.9% (1/17). Conclusions Single ventricle treatment remains the preferred procedure for patients with heterotaxy syndrome and its early and middle term results are satisfied.