BACKGROUND: Hyperhomocysteinemia (HHcy) has been linked to development of Alzheimer's disease (AD) neuropathologically characterized by the accumulation of amyloid ß (Aß). Microglia (MG) play a crucial role in uptake of Aß fibrils, and its dysfunction worsens AD. However, the effect of HHcy on MG Aß phagocytosis remains unstudied. METHODS: We isolated MG from the cerebrum of HHcy mice with genetic cystathionine-ß-synthase deficiency (Cbs-/-) and performed bulk RNA-seq. We performed meta-analysis over transcriptomes of Cbs-/- mouse MG, human and mouse AD MG, MG Aß phagocytosis model, human AD methylome, and GWAS AD genes. RESULTS: HHcy and hypomethylation conditions were identified in Cbs-/- mice. Through Cbs-/- MG transcriptome analysis, 353 MG DEGs were identified. Phagosome formation and integrin signaling pathways were found suppressed in Cbs-/- MG. By analyzing MG transcriptomes from 4 AD patient and 7 mouse AD datasets, 409 human and 777 mouse AD MG DEGs were identified, of which 37 were found common in both species. Through further combinatory analysis with transcriptome from MG Aß phagocytosis model, we identified 130 functional-validated Aß phagocytic AD MG DEGs (20 in human AD, 110 in mouse AD), which reflected a compensatory activation of Aß phagocytosis. Interestingly, we identified 14 human Aß phagocytic AD MG DEGs which represented impaired MG Aß phagocytosis in human AD. Finally, through a cascade of meta-analysis of transcriptome of AD MG, functional phagocytosis, HHcy MG, and human AD brain methylome dataset, we identified 5 HHcy-suppressed phagocytic AD MG DEGs (Flt1, Calponin 3, Igf1, Cacna2d4, and Celsr) which were reported to regulate MG/MΦ migration and Aß phagocytosis. CONCLUSIONS: We established molecular signatures for a compensatory response of Aß phagocytosis activation in human and mouse AD MG and impaired Aß phagocytosis in human AD MG. Our discoveries suggested that hypomethylation may modulate HHcy-suppressed MG Aß phagocytosis in AD.