Many functional magnetic resonance imaging (fMRI) studies have indicated that Granger causality analysis (GCA) is a suitable method for revealing causal effects between brain regions. The purpose of the present study was to identify neuroimaging biomarkers with a high sensitivity to amnestic mild cognitive impairment (aMCI). The resting-state fMRI data of 30 patients with Alzheimer's disease (AD), 14 patients with aMCI, and 18 healthy controls (HC) were evaluated using GCA. This study focused on the "triple networks" concept, a recently proposed higher-order functioning-related brain network model that includes the default-mode network (DMN), salience network (SN), and executive control network (ECN). As expected, GCA techniques were able to reveal differences in connectivity in the three core networks among the three patient groups. The fMRI data were pre-processed using DPARSFA v2.3 and REST v1.8. Voxel-wise GCA was performed using the REST-GCA in the REST toolbox. The directed (excitatory and inhibitory) connectivity obtained from GCA could differentiate among the AD, aMCI and HC groups. This result suggests that analysing the directed connectivity of inter-hemisphere connections represents a sensitive method for revealing connectivity changes observed in patients with aMCI. Specifically, inhibitory within-DMN connectivity from the posterior cingulate cortex (PCC) to the hippocampal formation and from the thalamus to the PCC as well as excitatory within-SN connectivity from the dorsal anterior cingulate cortex (dACC) to the striatum, from the ECN to the DMN, and from the SN to the ECN demonstrated that changes in connectivity likely reflect compensatory effects in aMCI. These findings suggest that changes observed in the triple networks may be used as sensitive neuroimaging biomarkers for the early detection of aMCI.