We developed a MATLAB algorithm to calculate reorganization energy utilizing rectilinear normal mode displacements. Normal mode‐projected rectilinear displacements and the corresponding angular frequencies, required for evaluating charge transfer reorganization energy within the harmonic oscillator approximation, were obtained from Cartesian coordinates and Cartesian force constant matrices determined with respect to the principal axes. To verify the algorithm developed with MATLAB, we compared the computed charge transfer reorganization energies to those evaluated by the DUSHIN program, and there was no substantial difference, indicating that our algorithm guarantees the numerical accuracy of the calculations. This algorithm was applied to design silicon quantum dots (Si QDs) with low reorganization energies for charge transfer.