We　propose　an　improved　transfer　entropy　approach　called　the　dynamic　version　of　the　force　constant　fitted　Gaussian　network　model　based　on　molecular　dynamics　ensemble　(dfcfGNMMD)　to　explore　the　allosteric　mechanism　of　human　mitochondrial　phenylalanyl-tRNA　synthetase　(hmPheRS),　one　of　the　aminoacyl-tRNA　synthetases　that　play　a　crucial　role　in　translation　of　the　genetic　code.　The　dfcfGNMMD　method　can　provide　reliable　estimates　of　the　transfer　entropy　and　give　new　insights　into　the　role　of　the　anticodon　binding　domain　in　driving　the　catalytic　domain　in　aminoacylation　activity　and　into　the　effects　of　tRNA　binding　and　residue　mutation　on　the　enzyme　activity,　revealing　the　causal　mechanism　of　the　allosteric　communication　in　hmPheRS.　In　addition,　we　incorporate　the　residue　dynamic　and　co-evolutionary　information　to　further　investigate　the　key　residues　in　hmPheRS　allostery.　This　study　sheds　light　on　the　mechanisms　of　hmPheRS　allostery　and　can　provide　important　information　for　related　drug　design.