This review systematically summarizes the research progress of ketamine and its interaction with specific brain regions in the context of neuropathic pain comorbid with depression. As a non-competitive inhibitor of N-methyl-D-aspartate (NMDA) receptors, Ketamine exerts complex mechanisms and controversial topic. The structure and function of NMDA receptors, as well as the binding sites of ketamine, are summarized, and the hypothesis of disinhibition and neuroplasticity of ketamine's antidepressant effect is elaborated. The mechanism of key brain regions, such as hippocampus and anterior cingulate cortex, is discussed in detail, and the antidepressant effect of ketamine is explored from the perspective of transcriptomics. Finally, this review integrates bioinformatics, molecular biology and other interdisciplinary approaches to elucidate the therapeutic effects and potential mechanisms of ketamine in treating neuropathic pain and depression comorbidity, providing a comprehensive theoretical basis, new directions for subsequent research and novel insights for the clinical application of ketamine.