The exhaust chimney of third-generation nuclear power units is a typical attached high-rise riser structure. In this paper, the simplified mechanical model and dynamic model of China’s third-generation nuclear power Hualong-1 VNA system, including multiple nonlinear factors, are established for the first time. The DTM (differential transformation method) was first applied to solve the natural vibration characteristics of a multi-point constrained variable cross-section riser structure, and the effects of variable cross-section, variable mass, variable axial force, and different elastic constraint parameters on the natural vibration characteristics of the system were studied. The dynamic behavior of the VNA system under the combined action of internal flow velocity, vortex excitation, and foundation excitation was studied. The results show that the outer diameter function of the VNA system pipeline should be designed as a quadratic function or a near quadratic multi-segment constant value function. The “limiting” effect of constraining large stiffness can force low-order vibration modes with high constraint stiffness to jump to high-order vibration modes with low constraint stiffness. The elastic constraint arrangement scheme with near center symmetry can make the system vibration mode present a half stable and half-curved form. A new optimization design scheme has been proposed regarding the layout and stiffness parameters of the VNA system guide bracket. This can enable the VNA system pipeline to avoid severe oscillations near the response extreme values caused by multiple frequency excitations of seismic loads under design and accident conditions and ensure the service life of the equipment.