The NO+MO/HF theory has been previously proposed to determine the nuclear and electronic wave functions in the ground state without the Born-Oppenheimer approximation. In this study, we apply the configuration interaction method with single particle excitation operators to the NO+MO/HF wave function. This method, named NO+MO/CIS method, gives not only the electronic excited state but also the vibrational excited state. Numerical applications of the NO+MO/CIS method to H-2, D-2, T-2, and H-3(+) molecules are performed and confirm its accuracy and feasibility.