We used cardiac magnetic resonance tissue tracking (CMR-TT) to quantitatively analyze the global, regional and layer-specific strain of isolated left ventricular noncompaction (ILVNC). Combined with late gadolinium enhancement (LGE), we initially explored the effect of focal myocardial fibrosis on myocardial strain. CMR was performed in 63 patients with ILVNC and 52 patients without ILVNC (i.e., the control group). The ILVNC group was divided into an LGE(+) group (29 patients) and an LGE(-) group (34 patients) according to the presence or absence of late gadalinum enhancement (LGE). CVI42 software was used to measure global and regional (basal, middle, apical) radial strain (RS), circumferential strain (CS), longitudinal strain (LS), subendocardial LS and subepicardial LS. The basal-apical strain gradient was defined as the apical mean strain minus the basal mean strain. We then compared differences between these strain parameters. The subendocardial-subepicardial LS gradient was defined as the maximum subendocardial LS minus the subepicardial LS. Compared with the control group, the global and regional RS, CS, LS and the subendocardial, subepicardial LS of the ILVNC group were significantly diminished (P < 0.01). Compared with the LGE(-) group, the global and regional RS, CS, LS and the subendocardial, subepicardial LS of the LGE(+) group were significantly diminished (P < 0.05). In the ILVNC group, the basal-apical CS and LS gradient, and the subendocardial-subepicardial LS gradient were significantly lower than those in the control group (P < 0.01). There were significant differences in myocardial strain between patients with and without ILVNC. ILVNC revealed a specific pattern in terms of strain change. The myocardial strain of the cardiac apex and endocardium was significantly lower than that of the cardiac base and epicardium, respectively. Myocardial strain reduction was more significant in ILVNC patients with focal myocardial fibrosis.