We show that the sizable D-term contributions to the sfermion mass spectrum can be signatures of a certain grand unified theory (GUT), E6×SU(2)F×U(1)A GUT. Note that these D-term contributions destroy the degeneracy of sfermion masses among different generations in this model. Such D-terms are strongly constrained by the FCNC processes if the SUSY breaking scale is the weak scale. However, in E6×SU(2)F×U(1)A, natural SUSY type sfermion mass spectrum is obtained, and if the masses of 103 sfermions are larger than O(1) TeV to realize 125 GeV Higgs and the other sfermion masses are O(10) TeV, then sizable D-term contribution is allowed. If the deviations by these D-terms can be observed in future experiments like 100 TeV proton collider or muon collider, we may confirm the E6×SU(2)F×U(1)A GUT.