Objective To investigate the connection between metabolic features and ultrastructure changes in hippocampus of APP / PS1 double transgenic mice, and to confirm whether this model is appropriate for Alzheimer’s disease (AD) research. Methods A novel object recognition test was conducted to compare learning and memory in APP / PS1 mice with age- and background-matched wild type mice. Metabolic features such as N-acetylaspartate (NAA), myo-Inositol (mI), choline (Cho), and glutamate (Glu) levels in the hippocampus were assessed using proton magnetic resonance spectroscopy. Cellular ultrastructures were observed using a transmission electron microscope. Results Compared with wild type mice, APP / PS1 mice exhibited significantly decreased learning and memory ability ( P < 0. 05), a significantly reduced NAA to creatine ( Cr) ratio ( P < 0. 05), and increased mI/ Cr and Cho / Cr (P < 0. 05 ) ratios in the hippocampus. Compared with wild type mice, APP / PS1 mice had the following features: mitochondria in neurons and astrocytes were irregularly shaped and condensed, there were more secondary lysosomes, astrocytes were over-active, and there were phagocytosed dystrophic neurites. Conclusions Pathological changes in NAA, mI, and Cho in the hippocampus of APP / PS1 mice could reflect abnormal inflammation and aberrant neurites evoked by beta amyloid in AD. Thus, APP / PS1 transgenic mice may represent a beneficial model for AD research.