With the development of the high-rise buildings, the columns with special cross-sectional shapes are frequently adopted for architectural and aesthetic purposes. The concrete filled steel tube (CFST) is a reasonable choice for such requirement due to the characteristics of excellent seismic performances, construction efficiency and strong adaptability to special shapes. This paper focuses on the seismic performance of a special-shaped hexagonal CFST column with an inner diaphragm plate and shear studs adopted in a super high-rise building. Experiments were conducted on five column specimens under axial compressive force and lateral cyclic loading to investigate the influence of various parameters including loading angle, axial compression ratio, shear studs and the type of in-filled concrete. In one of the specimens, the ultra-high performance concrete (UHPC) was used as the in-filled concrete to substitute the conventional normal strength concrete, and the effects on the capacity and ductility of the column were revealed. Then the failure mode, the load-deflection curves, seismic performance indexes and the strain distribution were analyzed. The flexural capacities of the columns were evaluated by the fiber section model, where the failure criterion considering the buckling of steel tube was proposed and the effects of studs were included. Finally, the contribution to axial force and bending moment from outer steel tubes, inner diaphragm plate and in-filled concrete were calculated and compared based on the proposed model. It is found that the fiber section model considering the steel plate buckling and strengthening effects of studs precisely predicted the moment-curvature curves and the flexural capacity of the test specimens. The contribution of the inner diaphragm plate was considerable which could not be neglected.