Objective: To compare 2D global strain between single left ventricle (SLV) group, single right ventricle (SRV) group after Fontan operation and normal healthy controls using feature tracking (FT) of cardiac magnetic resonance (CMR). Methods: Twenty two patients with single ventricle received Fontan operation with a mean age of (11.18±4.22) years and performing cardiac MRI(CMR) after Fontan operation between July 1, 2015 and January 30, 2017 were retrospectively analyzed. The mean year of MRI follow-up after surgery was (6.41±2.91) years. Of the 22 single ventricle patients, 6 were dominant left ventricle, 16 were 22 dominant right ventricle. Ten age-matched healthy children performing CMR were served as controls for providing reference values of strain. CMR function and ventricle strain comparisons were performed between SLV group, SRV group and control group. Bland-Altman method was used to compare the consistence among the groups. Results: End-diastolic volume index (117.79±56.82) mL versus (73.24±13.77) mL and ejection fraction(EF)(49.61±15.32)% versus (60.95±5.94)% were significantly different between healthy controls and Fontan operation repaired group(P<0.05). The comparison of SLV group and SRV group showed no significant difference in EF(49.00±17.68)% versus (48.0±13.77)% (P>0.05). In the comparison of strain among SLV, SRV and healthy control groups, the global longitudinal strain (-20.24±1.90) for SLV versus (-12.75±3.67) for SRV versus (-9.06±5.93) for controls was signi-ficantly different (P<0.05). The global longitudinal and circumferential strain of Fontan operation repaired groups had good consistence, and were better than radial strain. Conclusions: CMR-FT can be used as a method to evaluate cardiac function of complex congenital heart disease after Fontan operation. Compared with the ejection fraction, the 2D global longitudinal strain can be used as a reference value for evaluating the myocardial contraction function in single ventricle patients.