Background: The memory impairments in mild cognitive impairment (MCI) can be classified into encoding (EF) and retrieval (RF) failure, which can be affected by underlying pathomechanism. We explored the differences structurally and functionally.Methods: We compared quantitative electroencephalography (qEEG) power spectra and connectivity between 87 MCI patients with EF and 78 MCI with RF using iSyncBrain ™ (iMediSync, Inc., Korea) (https://isyncbrain.com/). Voxel-based morphometric analysis of the gray matter (GM) in the MCI groups and 71 cognitive normal controls were also done using the Computational Anatomy Toolbox 12 (http://www.neuro.uni-jena.de/cat/).Results: qEEG showed higher frontal theta and lower beta2 band power and higher theta and lower beta connectivity in the EF. There was no statistically significant difference in GM volume between the EF and RF. However, when compared to normal control, GM volume reductions due to EF in the left thalamus and bilateral hippocampi and reductions due to RF in the left thalamus, right superior frontal lobe, right superior temporal lobe, and right middle cingulum were observed ( p < 0.05, family-wise error correction). Conclusions: MCI differs functionally and structurally according to their specific memory impairments. The EF findings are structurally and functionally more consistent with the prodromal Alzheimer's disease stage than the RF findings. Since this study is a cross-sectional study, prospective follow-up studies are needed to investigate whether different types of memory impairments can predict the underlying pathology of amnestic MCI. Additionally, insufficient sample size may lead to ambiguous statistical findings in direct comparisons, a larger patient cohort could more robustly identify differences in GM volume reductions between the EF and the RF group.