This paper conducts an in-depth study on the dynamic stability and complex vibration behavior of a 12-pole active magnetic bearing (AMB) system considering gravitational effects under a PD controller. Firstly, based on electromagnetic theory and Newton’s second law, a two-degree-of-freedom control equation of the system, including PD control terms and gravitational effects, is constructed. This equation involves not only parametric excitation, quadratic nonlinearity, and cubic nonlinearity but also a more pronounced coupling effect between the magnetic poles due to the presence of gravity. Secondly, using the multi-scale method, a four-dimensional averaged equation of the system in Cartesian and polar coordinates is derived. Finally, through numerical analysis, the system’s amplitude–frequency response, motion trajectory, the relationship between energy and amplitude, and global dynamic behaviors such as bifurcation and chaos are discussed in detail. The results show that the PD controller significantly affects the system’s spring hardening/softening characteristics, excitation, amplitude, energy, and stability. Specifically, increasing the proportional gain can quickly suppress the rotor’s motion, but it also increases the system’s instability. Adjusting the differential gain can transition the system from a chaotic state to a stable periodic motion.