We develop the semi-closed orbit theory from two degrees of freedom to three non-separable degrees of freedom and put forward a new model potential for the Li Rydberg atom, which reduces the study of the system to an effective one-particle problem. Using this model potential and the closed orbit theory for three degrees of freedom, we calculate the recurrence spectra of Li Rydberg atom in perpendicular electric and magnetic fields. The closed orbits in the corresponding classical system have also been obtained. The Fourier transformed spectra of Li atom have allowed direct comparison between the resonance peaks and the scaled action values of closed orbits, whereas the nonhydrogenic resonance can be explained in terms of the new orbits created by the core scattering. Our result is in good agreement with the quantum spectra, which suggests that our calculation is correct.