An effective reduced-order model is presented in this paper for the vibration analysis of a mistuned blade–disc–shaft assembly considering the flexibility of the shaft and the rotordynamic effects. For the sake of accurate modeling and quantitative analysis, three-dimensional (3D) finite element models were employed in obtaining the governing equations of motion with the Coriolis force, centrifugal stiffening, and spin softening effects taken into account. Then, an efficient model order reduction technique based on the coordinate projection by normal modes of tuned assembly and cyclic symmetry analysis was developed for mistuned blade–disc–shaft assembly. The criterion of whether one matrix could be incorporated in cyclic symmetry analysis is presented. During the modeling, the mistuning in blade and disc was taken into account and dealt with independently. In mistuning projection, the blade and disc parts were both projected onto their tuned counterparts of the sector model, where the boundary conditions were set to be fixed and free, respectively. Finally, an example of a blade–disc–shaft assembly was employed to validate the effectiveness of the presented method in free and forced vibration analysis.