Three-dimensional space vector modulation (3DSVM) is proposed for controlling a three-leg centre-split inverter, which is used as a shunt power quality compensator for a three-phase four-wire system. Important issues for 3DSVM, such as 3D space vector allocation, zero-sequence compensation and DC voltage variation, are discussed in detail. In the two-level three-leg centre-split system, all eight vectors contribute to the zero-sequence compensation, which is different from the conventional two-dimensional compensation. Hence, the 3DSVM control strategy is more complicated than conventional 2DSVM. Particularly, in a two-level system there is no null vector in 3D case such that the zero state is approximated by two zero vectors, which directly point in positive and negative zero-axis, respectively. Results indicate that the original reference of the 3D vector's allocation is affected by DC voltage variation only along the zero-frame. Conversely, the DC voltage variation can be controlled by adjusting the origin of 3D reference. Simulation results are given to show the validity of the proposed control strategy: 3DSVM with DC voltage variation control. A two-level three-leg centre-split inverter prototype is implemented and controlled by a digital signal processor with 2.5 kHz switching frequency. Experimental results are also presented to show its validity.