Evidence suggests interplay among the three major risk factors for Alzheimer’s disease (AD): age, APOE genotype, and sex. Here, we present comprehensive datasets and analyses of brain transcriptomes and blood metabolomes from human apoE2-, apoE3-, and apoE4-targeted replacement mice across young, middle, and old ages with both sexes. We found that age had the greatest impact on brain transcriptomes highlighted by an immune module led by Trem2 and Tyrobp, whereas APOE4 was associated with upregulation of multiple Serpina3 genes. Importantly, these networks and gene expression changes were mostly conserved in human brains. Finally, we observed a significant interaction between age, APOE genotype, and sex on unfolded protein response pathway. In the periphery, APOE2 drove distinct blood metabolome profile highlighted by the upregulation of lipid metabolites. Our work identifies unique and interactive molecular pathways underlying AD risk factors providing valuable resources for discovery and validation research in model systems and humans. Display omitted •Aging leads to the most profound changes in brain gene expression networks•Immune module led by Alzheimer’s risk genes Trem2/Tyrobp is upregulated with aging•Alzheimer’s risk allele APOE4 increases the expression of Serpina3 family genes•Alzheimer’s protective allele APOE2 drives unique serum metabolome profiles Zhao et al. present comprehensive datasets and analyses of brain transcriptomes and blood metabolomes from human apoE2-, apoE3-, and apoE4-targeted replacement mice across young, middle, and old ages with both sexes. The study provides critical insight on the molecular pathways underlying three major Alzheimer’s risk factors age, APOE, and sex.