Here we aimed at exploring the effect of hypoxia on cognitive impairment progression in a single cell resolution through single cell RNA sequencing (ScRNA seq). We exposed the APP/SP1 transgenic AD model mice to hypoxia condition and explored the cell heterogeneity and interactions in cerebral cortex with single cell RNA sequencing (10X genomics). We further analyze the differently expressed genes and signaling pathways related with cognitive impairment by different cell types and subclusters.