To summarize clinical predictors and imaging characteristics of critically ill children infected with SARS-CoV-2 Omicron with neurological complications in Shenzhen during the peak of the first round of infections. The clinical data of 11 critically ill children with neurological complications infected with SARS-CoV-2 Omicron in Shenzhen Children's Hospital from December 12 to 31, 2022, were retrospectively collected and analyzed. Laboratory test results related to liver parenchymal injury, histiocytic injury, inflammation, and coagulation function were collected, and imaging characteristics including CT and/or magnetic resonance imaging (MRI) were analyzed. The differences in CT/MRI score, acute necrotizing encephalopathy severity scale (ANE-SS) score and total score (CT/MRI score + ANE-SS score) were compared between the two groups with different prognosis during hospitation. Among 11 children, 7 were male and 4 were female. The age ranged from 10 months to 16 years. There were 5 cases of acute necrotizing encephalopathy (ANE) and 6 cases of acute fulminant cerebral edema (AFCE). During hospitalization, 3 patients survived and 8 patients died of multiple organ dysfunction syndrome (MODS), including 2 cases of ANE and 6 cases of AFCE. All cases had fever (> 38.5 centigrade), and 3 cases had ultra-high fever (> 41 centigrade). Within 48 hours of onset, all cases had disorders of consciousness and 9 cases had seizures. The 8 dead children had complications with multisystem involvement, including shock, respiratory failure, disseminated intravascular coagulation (DIC), liver failure, renal failure or myocardial damage, and the laboratory predictors related to hepatocellular injury [alanine aminotransferase (ALT), aspartate aminotransferase (AST)], histocyte injury [creatine kinase (CK), lactate dehydrogenase (LDH)], inflammation [procalcitonin (PCT), interleukin-6 (IL-6), serum ferritin (SF)], coagulation function (D-dimer) and blood glucose (Glu) increased in different quantities, of which PCT was specifically increased in 6 cases with AFCE, PLT was specifically decreased in 3 cases with AFCE, and ALT and LDH were significantly increased in 2 cases with ANE. Imaging analysis showed subarachnoid hemorrhage, basal ganglia and thalamus lesions in all 6 cases with AFCE, while thalamus lesions in all 5 cases with ANE. The ANE-SS score of 8 deceased children ranged from 2 to 7 (of which 6 cases were ≥ 5), and the ANE-SS score of 3 surviving children ranged from 0 to 2. Eight dead children had a CT/MRI score of 1-4 (of which 6 cases were 4), and 3 surviving children had a CT/MRI score of 1-2 (of which 2 cases were 1). The total score of 8 deceased children was 6-10 (of which 6 cases ≥ 8), and 3 surviving children was 1-4. The neurological complications of critically ill children infected with SARS-CoV-2 Omicron in Shenzhen progressed rapidly to ANE and AFCE, with high mortality. High fever (> 40 centigrade), convulsion/disturbance of consciousness, and multiple organ failure were the most common symptoms in ANE and AFCE cases. PCT increased and PLT decreased specifically in AFCE cases. Poor prognosis (death) was more common in age < 4 years old, predictors of ALT, AST, CK, LDH, PCT, D-dimer, Glu, IL-6 increased significantly, PLT decreased significantly. The common imaging feature of ANE and AFCE is the involvement of dorsal thalamus, a new imaging sign of AFCE (subarachnoid hemorrhage) was found. The higher the ANE-SS score, CT/MRI score and total score, the greater the risk of death.