The stability and bifurcation of a flexible 3D rotor system are investigated in this paper. The rotor is discretized by 3D elements and reduced by using component mode synthesis. Periodic motions and stability margins are obtained by using the shooting method and path-following technique, and the local stability of the periodic motions is determined by using the Floquet theory. Comparisons indicate that 3D and 1D systems have a general resemblance in the bifurcation characteristics while mass eccentricity and rotating speed are changed. For both systems, the orbit size of the periodic motions has the same order of magnitude, and the vibration response has identical frequency components when typical bifurcations occur. The stress distribution and location of the maximum stress spot are determined by the bending mode of the rotor. The type of 3D element has a slight effect on the stability and bifurcation of the rotor system. Generally, this paper presents a feasible method for analyzing the stability and bifurcation of complex rotors without much structural simplification.