Copper accumulation-induced cognitive impairment represents a significant clinical manifestation in patients with Hepatolenticular Degeneration (HLD). Neurotransmitters play a crucial role in cognitive function, but the effects of their metabolic changes in different brain regions on cognitive dysfunction remain unclear. Thus, we employed desorption electrospray ionization mass spectrometry imaging (DESI-MS) to observe molecular metabolic disturbances and spatial distribution in the brains of copper-loaded rats. The results showed that there were certain changes in metabolic substance levels in nine brain regions of copper-loaded rats, and the cortical region showed the most significant changes, including increased levels of glutamine, adenosine, taurine, and other substances; and decrease levels of γ-aminobutyric acid, hypoxanthine, and other substances. Collectively, these changes suggest disruptions in the glutamine (Gln)-glutamate (Glu)/γ-aminobutyric acid (GABA) cycle. Notably, Gandouling tablets (GDL) intervention restored cognitive abilities in the water maze and reduced copper levels. This study highlights that copper accumulation may induce cognitive deficits by disrupting neurotransmitter balance; conversely, GDL may protect cognitive function by restoring this balance.