Abstract: The drill-string vibration in deep wells is a critical factor that compromises drilling safety and limits efficiency. Theoretical modeling, an essential tool for studying vibration characteristics and drivers, is limited by ambiguities in damping calculations and by uncertainties in parameter selection. Existing damping approaches are systematically analyzed, and a multi-degree-of-freedom axial–torsional coupled model that includes nonlinear bit–rock interaction is established. Based on Rayleigh damping theory, the vibration responses across ranges of damping ratios and of natural frequencies are examined. Monte Carlo–based uncertainty analysis reveals a nonlinear relationship among damping ratios, natural frequencies, and Rayleigh damping coefficients, which can cause deviations in numerical simulations. To mitigate parameter uncertainty, a modal-segmented damping method is proposed. The method assigns a damping ratio to each mode and superposes modal contributions, addressing the subjectivity in damping-ratio selection and the ambiguity in modal-order selection inherent in Rayleigh damping. This enhances the model’s rigor and predictive reliability. The comparison of simulations with field measurements shows that the method captures drill-string vibration characteristics, with close agreement between calculated and measured data. The method also scales to the vibration analyses of various drill-string configurations.