Isolated left ventricular non-compaction (LVNC) is a rare cardiomyopathy that leads to severe clinical complications. This study is to investigate whether or not prolonged QTc is a good indicator for evaluating the severity of fibrosis and predicting the prognosis of LVNC, and if native T1 can be used to quantify the fibrosis. 32 LVNC patients and 14 healthy controls with matched age and sex were examined by CMR and ECG to acquire native T1, QTc interval, and ECG abnormalities. 18 LVNC patients had normal QTc and 14 LVNC patients had prolonged QTc. The mean native T1 value of the normal controls, normal QTc and prolonged QTc patients was 1096.0 ± 41.5, 1141.98 ± 45.46, and 1182.67 ± 42.02 ms, respectively. One-way ANVOA showed significant differences in native T1 among three groups (F = 14.9, p < 0.001). In LVNC patients, the QTc interval significantly correlated with LVEF (p = 0.003, r = 0.51) and native T1 values (p = 0.015, R = −0.47). This suggests that prolonged QTc is associated with more severe compacted myocardial fibrosis, more cardiac dysfunction, and a poorer prognosis in LVNC patients. Follow-up data showed significant differences in adverse events between patients with normal QTc and patients with prolonged QTc (p = 0.036). Prolonged QTc interval leads to more severe compacted myocardial fibrosis, poorer cardiac dysfunction, and poorer prognosis in LVNC patients.