Objectives: This study examined the effects and molecular mechanisms of deep hypothermic low flow (DHLF) on brain tissue in three genotypes of 3-week-old C57BL/6 mice (N = 180).Methods: Mice in the model condition were subjected to cerebral ischemia-reperfusion (I-R) while undergoing DHLF, then reperfused and rewarmed. Brain tissue damage was measured with 2,3,5-triphenyltetrazolium chloride (TTC) staining, and protein expression was measured by Western blot at 2 h, 24 h, and 72 h after treatment; messenger ribonucleic acid (mRNA) expressions were measured by real-time polymerase chain reaction (PCR) at 2 h, 24 h, and 72 h.Results: The expressions of p-Akt1 and p-GSK-3β were significantly higher in the model condition than the condition across genotypes, but both were significantly lower in the Akt1 mice. The expressions of Akt1 mRNA and Akt3 mRNA, but not Akt2 mRNA, were significantly higher in the model condition across genotypes. Brain damage was significantly greater in the Akt1 knockout gene mice compared with Akt2 gene knockout and wild type mice at 24 h and 72 h.Conclusion: These results suggest that the neuroprotective effects of DHLF reflect increased expression of p-GSK-3β induced through the PI3K/Akt signal pathway. Findings of real-time PCR imply that Akt1 mRNA and Akt3 mRNA may influence the expression of p-Akt1 and p-GSK-3β in mice undergoing DHLF.