Objective Clinical manifestations of left ventricular noncompaction (LVNC) in children lack specificity. At present, there are relatively few systematic studies on the prognostic risk factors of LVNC, and clear evidence for risk stratification is still lacking in clinical practice. This study aimed to analyze the clinical characteristics, genetic variations, and prognostic factors of LVNC in children. Methods Clinical data of 42 children diagnosed with LVNC from June 2018 to June 2024 were retrospectively analyzed. According to the occurrence of adverse cardiovascular events during follow-up, they were divided into an adverse event group (15 cases) and a non-adverse event group (27 cases). Clinical and laboratory indicators were compared between the two groups, and multivariate Logistic regression was used to analyze prognostic risk factors. Results Among the 42 children, 24 were males (57.1%), with a median age of 92.5 months at diagnosis. The common initial symptoms were poor appetite accompanied by shortness of breath (19.0%), chest tightness or chest pain (19.0%), and palpitations (16.7%). At the initial diagnosis,children with cardiac function class III/IV accounted for 35.7% (15/42).92.9% (39/42) of the children had abnormal electrocardiograms (ECG), with tachyarrhythmia being the most common (14/42). Echocardiography revealed left atrial and left ventricular enlargement in 71.4% (30/42) and 80.9% (34/42) of patients, respectively. The median left ventricular ejection fraction (LVEF) was 52.0% (41.8-62.0), and the median non-compacted to compacted (NC/C) ratio was 2.5 (2.1-3.0). Four children had a family history of sudden death or cardiomyopathy in first-degree relatives. 16 children underwent genetic testing, and pathogenic gene mutations were detected in 10 cases. The median follow-up duration was 30 months, the fatality rate was 9.5%, and symptoms improved in 45.2% (19/42) of children. The group with adverse events exhibited a significantly higher incidence of tachyarrhythmia, a greater proportion of patients with cardiac function class III/IV, and higher NC/C ratios compared to the group without adverse events (P<0.05). Multivariate logistic regression analysis demonstrated that cardiac function class Ⅲ/IV (OR=13.55, 95% CI: 1.87~98.39, P= 0.01), tachyarrhythmia (OR=19.73, 95% CI: 2.28~170.47, P=0.007), and an elevated NC/C ratio (OR=5.19, 95% CI: 1.20~22.40, P=0.027) as independent risk factors for an unfavorable prognosis. Conclusions Children with LVNC exhibit strong heterogeneity in clinical manifestations and are often associated with a genetic background. Poor cardiac function, tachyarrhythmia, and a high NC/C ratio are independent risk factors for poor prognosis, so intensive monitoring and intervention for highrisk children are required in clinical practice.