As　the　4　allele　of　apolipoprotein　E　(APOE4)　is　proved　a　high　risk　factor　of　Alzheimer＇s　disease　(AD),　numerous　studies　have　used　modalities　of　neuroimaging　data　to　investigate　the　alterations　of　brain　caused　by　APOE4.　A　recent　study　has　shown　that　APOE4-related　pathological　changes　of　cortical　networks　during　rest　exist　in　APOE4　carriers.　However,　the　interrelationship　among　the　resting　intrinsic　networks　(ICNs)　has　not　been　adequately　explored.　In　the　present　study,　seven　ICNs　were　detected　in　both　of　APOE4　carriers　and　APOE4　non-carriers　with　spatial　independent　component　analysis　(ICA).　Then　the　effective　connectivity　patterns　of　the　two　groups　were　acquired　using　multivariate　Granger　causality　analysis　(mGCA)　the　results　of　which　reflect　the　information　flow　among　ICNs.　Compared　with　APOE4　non-carriers,　significant　difference　in　activity　was　found　within　default　mode　network　in　APOE4　carriers.　Moreover,　the　significantly　reduced　intensity　of　causal　interaction　from　auditory　network　to　cerebellum　network　was　found　in　APOE4　carriers.　And　we　found　the　significantly　causal　relationship　from　cerebellum　network　to　default　mode　network　only　existed　in　the　connectivity　pattern　of　APOE4　carriers　but　not　in　that　of　APOE4　non-carriers.　In　addition,　the　subcortical　network　and　cognitive　control　network　in　APOE4　carriers　were　found　less　influenced　by　other　ICNs.　The　findings　in　our　study　suggest　that　APOE4　indeed　modulates　the　activities　and　interactions　of　ICNs,　which　might　be　the　genetic　cause　of　the　dysfunctional　process　in　APOE4　carriers.　Our　findings　may　shed　new　light　on　the　ways　how　APOE4　affects　the　functions　of　nervous　systems　and　provide　a　perspective　to　understand　genetic　basis　of　pathogenesis　of　AD.　©　2017　IEEE.