Three-tower self-anchored suspension bridge (TSSB) is more and more favored because of its beautiful structure and strong adaptability to terrain and geological conditions. However, there are few engineering practices and related researches on super long-span three-tower self-anchored suspension bridges. A three-dimensional finite element model for the Fenghuang Yellow River Bridge, with the world’s longest span of its kind under construction, is established using the ANSYS finite element program, and the structural dynamic characteristics of the super long-span TSSB are studied and compared with those of several bridges of the same type or with similar spans. In addition, the influence of the key design parameters such as the stiffening girder stiffness, tower stiffness, main cable and suspender stiffness, central buckle, and longitudinal constraint system on the dynamic characteristics of the structure is analyzed. The results show that the first mode of the TSSB is longitudinal floating, the lower-order modes are dominated by vertical bending modes, while the higher-order modes are primarily vibration modes of the main cables, and the torsional modes exhibit strong coupling with the lateral sway of the towers and main cables. The frequency of the first antisymmetric vertical bending mode of the TSSB has an inversely proportional relationship with the main span length. Compared with a double-tower ground-anchored suspension bridge and cable-stayed bridge with similar spans, the TSSB has the lowest frequency for the first antisymmetric vertical bending mode and the highest frequency for the first symmetric vertical bending mode, with a more pronounced coupling with the towers and main cables in the torsional modes. Analysis of the structural parameters shows that the frequencies of the longitudinal floating mode, first antisymmetric vertical bending mode, first symmetric vertical bending mode, and first torsional mode are most sensitive to the longitudinal bending stiffness of the side tower, central buckle, vertical bending stiffness of the stiffening girder, and torsional stiffness of the stiffening girder, respectively. The research findings and relevant conclusions can provide basic data for response analysis of long-span TSSBs under dynamic loads and offer an engineering reference for the design of similar bridges around the world.