In this paper, a new energy decomposition analysis scheme based on the generalized Kohn-Sham (GKS) and the localized molecular orbital energy decomposition analysis (LMO-EDA) scheme, named GKS-EDA, is proposed. The GKS-EDA scheme has a wide range of DFT functional adaptability compared to LMO-EDA. In the GKS-EDA scheme, the exchange, repulsion, and polarization terms are determined by DFT orbitals; the correlation term is defined as the difference of the GKS correlation energy from monomers to supermolecule. Using the new definition, the GKS-EDA scheme avoids the error of LMO-EDA which comes from the separated treatment of E-X and E-C functionals. The scheme can perform analysis both in the gas and in the condensed phases with most of the popular DFT functionals, including LDA, GGA, meta-GGA, hybrid GGA/meta-GGA, double hybrid, range-separated (long-range correction), and dispersion correction. By the GKS-EDA scheme, the DFT functionals assessment for hydrogen bonding, vdW interaction, symmetric radical cation, charge-transfer, and metal-ligand interaction is performed.