Considering the isolobal analogy between two fragments CH and BCO, the calculations on the reactants,products, and transition states for the Claisen rearrangement of (BCO)n -substituted phenyl allyl ethers at the B3P86/6-311+G** level was performed in this study. The transition states of (BCO)n-substituted systems have looser and more structures with dipole nature. The substitutions of CH by BCO do favor the reduction of the free energies of activation and the enhancement of stabilization of both reactants and products. A Marcus theory and frontier molecular orbitals were used to separate the thermodynamic and intrinsic contributions to the activation energies.