Among hundreds of spinel oxides, LiTi2O4 (LTO) is the only one that exhibits superconductivity (Tc ~13 K). Although the general electron-phonon coupling is still the main mechanism for electron pairing in LTO, unconventional behaviors such as the anomalous magnetoresistance, anisotropic orbital/spin susceptibilities, etc. reveal that both the spin and the orbital interactions should also be considered for understanding the superconductivity. Here, we investigate tunneling spectra of [111]-, [110]- and [001]-oriented high quality LTO thin films. Several bosonic modes in tunneling spectra are observed in the [111]- and [110]-oriented films but not in [001]-oriented ones, and these modes still exist at T = 2Tc and beyond the upper critical field, which are confirmed as stemming from electron-phonon interaction by DFT calculations. These modes only appear in special surface orientations, indicating that the electron-phonon coupling in LTO system is highly anisotropic and may be enhanced by orbital-related state. The anisotropic electron-phonon coupling should be taken seriously in understanding the nature of LTO superconductivity.