In summary, with three prototypical shared proton systems, H 5 O + 2 , H 3 O - 2 and AHA -, we demonstrated that our CNEO methods can accurately and efficiently describe the proton transfer modes in shared proton systems. In all three systems, CNEO-DFT accurately predicted the proton to be shared equally by the two ending groups whereas pure electronic DFT with classical treatment on nuclei often cannot. Based on the physically correct geometries, both CNEO harmonic analysis and CNEO-MD can well describe the key features related to fundamental transitions in the IR spectra, which is greatly superior to the conventional DFT harmonic analysis, DFT-VPT2, and conventional DFT-based AIMD. Although the descriptions of overtones, combination bands, and Fermi resonances are still challenging and high-level quantum methods such as MCTDH and VSCF/VCI are still needed for the accurate description of these subtle features, our CNEO methods excel in their abilities to accurately and efficiently capture the key fundamental transition natures in relatively large systems. Therefore, CNEO methods are promising for future applications to larger and more complex systems like biological systems and materials systems in which proton transfer plays a crucial role.