The cellular and molecular mechanisms associated with hippocampal impairments due to MA remain unknown. In this study, the effects of MA on structural alterations and gene expressions in the hippocampus were investigated. We analyzed the pattern of volumetric changes in the hippocampus using magnetic resonance imaging (MRI) after acute and chronic administration of MA to cynomolgus macaques (Macaca fascicularis). In addition, we performed large-scale transcriptome profiling in the hippocampus using RNA-Seq technology to identify differentially expressed genes (DEGs) and their regulatory mechanisms affected by MA. The hippocampus in response to acute and chronic MA exhibited a significant volumetric atrophy compared with the hippocampus of controls. Based on gene ontology (GO) analysis, the genes associated with vesicle localization were upregulated and the genes associated with cytoskeleton organization and phagocytosis were downregulated in the acute MA-treated group compared to the control group. Conversely, genes associated with regulation of cell proliferation and angiogenesis were upregulated in the chronic MA-treated group, while genes associated with synaptic transmission, regulation of neuron differentiation and regulation of neurogenesis were downregulated in the chronic MA-treated group. We confirmed that expression patterns for some genes were similar to the results from RNA-Seq based on RT-qPCR.These results not only aid the understanding of cellular and molecular mechanisms regulated by MA in the hippocampus but also suggest basic information aiding biomarker and novel drug development for treating hippocampal impairment caused by MA abuse