Gap between the steel tube and core concrete of Concrete-Filled Steel Tube (CFST) members is regarded as an initial imperfection, which may exist in the CFST arch bridge due to construction process problems. In this paper, based on the design scheme of the bolt-welded joints in arch rib columns of an extra-long span CFST arch bridge, the effects of two types of initial imperfections, interfacial gap and spherical-cap gap, on the mechanical properties of Bolt-Welded CFST (BWCFST) short column under axial compression were investigated. Axial compression tests were conducted on three column specimens with spherical-cap gap, three specimens with interfacial gap, and one normal specimen without imperfection. A Finite Element Analysis (FEA) model was developed to further investigate the behavior of the BWCFST short columns, and was validated by the experiment.