The construction and assembly of an axial compressor blade row introduces real geometric features, which leads to the deviation of flow characteristics from the intended design. According to the realistic assembly errors observed in the four-stage low-speed research compressor developed by Shanghai Jiao Tong University, two representative step geometries at the rotor platform were abstracted. Unsteady simulations were carried out in the stage environment to study the influence of hub discontinuities on compressor performance and loss mechanisms. The comparisons of smooth hub, elevated hub (EH), and a wedged hub (WH) demonstrated that all the step geometries resulted in increased loss inside both rotor and stator rows. The loss induced by WH was more sensitive to step heights than EH. Under the influence of forward facing step, rotor incidence was reduced and horseshoe vortex (HV) was exacerbated, leading to the accumulation and separation of low momentum fluids at the pressure side corner. This led to a redistribution of losses across the span. In the lower half span, the relative total pressure loss increased almost linearly with step heights, while in the tip region, it reduced slightly. The backward facing step generated the step corner vortices (SCV) that shed and propagated downstream. The SCV interacted with the HV and cavity leakage vortex in the stator passage. Coupled with the augmented stator inflow angle, the corner separation at the suction side was dramatically intensified and led to a significant loss increase.