The vibration reduction performance of composite honeycomb hemispherical shells (CHHSs) coated with functional gradient protection coating (FGPC) are investigated in this work. Using the first-order shear deformation theory and the power-law distribution rule, the virtual spring technique, the regional decomposition method, and the Newmark-Beta approach, etc., a dynamic model of the FGPCCHHSs under base excitation is formulated to solve the inherent characteristics and displacement responses in time and frequency domains. After a set of convergence analyses are completed to ascertain an appropriate segment number and the stiffness values of virtual springs employed in the predictive model, the forecasted vibration parameters are verified using the literature and experimental results that are performed on uncoated and coated shells. The maximal natural frequency errors of the current model compared to the experimental results are 3.8% and 4.8%, and the displacement response errors under different excitation amplitudes are less than 10.3% and 12.7%, respectively, which demonstrate the correctness of such a model. Finally, the impact of key structural and material parameters on the vibration behaviors of the FPGCCHHSs is evaluated. To improve their vibration suppression capability, it is recommended to choose a high gradient index of coating material and a large thickness ratio of the FGPC to the overall shell with a reasonable moduli ratio of Material A to Material B of the FGPC to improve vibration reduction capability. This study offers a practical model tool and several important design recommendations for vibration prediction and dynamic attenuation of honeycomb sandwich hemispherical shell structures in aerospace engineering.