Three-level shunt power quality conditioner (SPQC) is widely used for compensation of unbalanced or harmonic current due to the general application of non-linear loads in three-phase four-wire system. To better analyse two mainstream topologies of SPQC, three-leg centre-split topology and four-leg topology, a unified topology is proposed in this paper, which offers significant instructions on appropriate topology selection and circuit parameters optimization under different application scenarios. Quantitative comparison on compensation effect on the certain condition is also available by the proposed topology. Since the additional zero sequence current control for neutral point oscillation reduction have negative effect on current compensation, a kind of alternative method by adjusting pulse sequence of power devices in modulation strategies is introduced. Theoretical results and effectiveness of methods are validated by simulations with PSCAD/EMTDC.