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Abstract INTRODUCTION The precise apolipoprotein E (APOE) ε4‐specific molecular pathway(s) for Alzheimer's disease (AD) risk are unclear. METHODS Plasma protein modules/cascades were analyzed using weighted gene co‐expression network analysis (WGCNA) in the Alzheimer's Disease Neuroimaging Initiative study. Multivariable regression analyses were used to examine the associations among protein modules, AD diagnoses, cerebrospinal fluid (CSF) phosphorylated tau (p‐tau), and brain glucose metabolism, stratified by APOE genotype. RESULTS The Green Module was associated with AD diagnosis in APOE ε4 homozygotes. Three proteins from this module, C‐reactive protein (CRP), complement C3, and complement factor H (CFH), had dose‐dependent associations with CSF p‐tau and cognitive impairment only in APOE ε4 homozygotes. The link among these three proteins and glucose hypometabolism was observed in brain regions of the default mode network (DMN) in APOE ε4 homozygotes. A Framingham Heart Study validation study supported the findings for AD. DISCUSSION The study identifies the APOE ε4–specific CRP–C3–CFH inflammation pathway for AD, suggesting potential drug targets for the disease. Highlights Identification of an APOE ε4 specific molecular pathway involving blood CRP, C3, and CFH for the risk of AD. CRP, C3, and CFH had dose‐dependent associations with CSF p‐Tau and brain glucose hypometabolism as well as with cognitive impairment only in APOE ε4 homozygotes. Targeting CRP, C3, and CFH may be protective and therapeutic for AD onset in APOE ε4 carriers.