An analysis approach that based on the Granger causality method is proposed to study the directional effective influence between brain regions in the fMRI data. Granger causality was employed to extracted BOLD signals to investigate effective connectivity inthe brain network. Data from an emotion task were used to validate this method, and the emotion pathway was partly clarified illustrated focus on the right amygdala. The presented results, exploring directional influences between activated brain regions, indicated that the Granger causality mapping combined with spectral matrix factorization and principal component analysis in the frequency domain could improve upon existing applications of traditional pairwise Granger causality mapping method in human brain effectiveconnectivity studies.