Layered transition metal dichalcogenides (TMDs) have aroused extensive interest due to their remarkable electronic, optical, and mechanical properties. Among them, molybdenum disulfide (MoS2) exhibits two main stacking polytypes: the centrosymmetric 2H phase and the non-centrosymmetric 3R phase. The latter has recently received attention due to its spontaneous polarization, piezoelectricity, band modulation, and possible topological features, but its lattice dynamics and phonon-related properties are still poorly understood. To address this gap, in this work, we comprehensively study the layer-dependent Raman phonon characteristics of 3R-phase MoS2 and systematically compare them with those of the 2H phase. Experimentally, we employ confocal Raman spectroscopy and polarization-resolved second-harmonic generation (SHG) to probe vibrational modes and stacking-dependent nonlinear responses of samples ranging from monolayer to bulk. The SHG measurements provide a clear method for distinguishing stacking orders: although the SHG signals disappear in even-layer 2H samples due to inversion symmetry, they strongly exist in 3R samples of any thickness. The Raman spectra in the low-frequency region reveal different shear and breathing modes, and the evolution of these modes with layer number is analyzed using a linear chain model (LCM) and a more refined force constant model (FCM). Although the LCM qualitatively captures the layer-dependent shifts of interlayer vibrations, the FCM provides quantitative agreement with experiments by explicitly combining the nearest neighbors and the next-nearest-neighbor interactions as well as surface corrections. To further explain the relative intensities of interlayer Raman modes, we introduce the bond polarization model (BPM), which links mode-dependent scattering strength to the symmetry and orientation of chemical bonds. Our BPM analysis reveals the pronounced asymmetry in charge redistribution for 3R stacking, leading to weaker interlayer binding energy than 2H (0.111 eV vs. 0.113 eV), and consequently a lower sliding barrier, which is consistent with the observed propensity of 3R crystals for interlayer slip. In the high-frequency region, both stacking types show characteristic in-plane and out-of-plane modes. However, the peak separation in 3R-phase MoS2 demonstrates stronger sensitivity to the layer number, making it a more reliable spectroscopic fingerprint for thickness identification. Importantly, it is found that surface effects play a critical role in reproducing experimental high-frequency shifts in 3R samples, reflecting their weaker interlayer coupling and enhanced surface contributions. In summary, this work establishes a complete picture of the phonon behavior in 3R-phase MoS2, effectively bridging experiment and theory. Our results indicate that Raman spectroscopy combined with SHG provides a powerful toolkit for identifying stacking order and thickness in layered MoS2. By benchmarking LCM, FCM, and BPM models, we clarify the roles of interlayer coupling, stacking symmetry, and surface effects in shaping vibrational properties. These insights not only deepen the fundamental understanding of lattice dynamics of non-centrosymmetric TMD polytypes, but also lay the foundation for the development of 3R-phase MoS2 in next-generation optoelectronic, piezoelectric, and quantum devices.
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