The invention discloses a space vector pulse width modulation (SVPWM) interleaving system and an interleaving control method thereof. The interleaving system comprises a first power module and a second power module, wherein the first power module and the second power module both employ two-level three-phase fully-controlled bridge topological structures. The interleaving control method comprises a starting procedure and an interrupt procedure, wherein the starting procedure comprises energizing the interleaving system, initializing a register, setting a continuous increase and decrease mode of a timer, judging a power module of executing the procedure, inquiring whether the power modules are standard and synchronous or not and enabling the timer to be interrupted, and the interrupt procedure comprises calculating and inputting a modulation wave, performing three seconds coordinate conversion, judging a sector, calculating action time of adjacent vectors and comparing corresponding loading of the register. The interleaving system and the interleaving control method have the advantages that an interleaving idea is transplanted to an SVPWM algorithm, the DC voltage utilization ratio of the interleaving system is improved, and the output waveform quality of the interleaving system is improved.