A new method of comparing and analyzing the electrostatic potential (ESP) charges of the common atom or group to evaluate and compare the stabilities of covalent compounds was introduced. That is, covalent compounds will become more stable when the electron acceptors accept adequate electrons and possess adequate negative charges, and the electron donors donate adequate electrons and possess adequate positive charges accordingly. All calculations were performed by density functional theory (DFT) and the general gradient approximation (GGA) method with the Beck-LYP hybrid functional and the DNP basis set in Acceryls' code Dmol3. Calculation results verified the method considering the molecular structure is well applied in the covalent molecule systems of hydrides, oxides, alkyl radicals, and nitro compounds. Furthermore, the method has good operability, for the charges can be easily obtained by simple calculation.