The invention provides a control method and system for a power electronic transformer. The method includes the steps that S1, an active current instruction value of the power electronic transformer is determined, and active power which the power electronic transformer needs to output is controlled; S2, a reactive harmonic current instruction value of the power electronic transformer is determined; S3, according to the active current instruction value and the reactive harmonic current instruction value, a recombination current instruction value of the power electronic transformer is determined; S4, the current of the power electronic transformer is detected; S5, the output current of the power electronic transformer is controlled to follow the recombination current instruction value through a current control algorithm. The power electronic transformer and a traditional transformer operate in a parallel connection mode, while the load active power is provided, the quality of electric energy of a low-voltage grid is adjusted, distribution network contamination is eliminated, and stability and power supply reliability of a power distribution system are improved.