The invention discloses a cooperative control method of a power electronic system. A large current limit inductor is connected with a primary side of a coupling transformer of a series active power filter in parallel; and by utilizing the cooperative control method, the series active power filter compensates harmonic voltage during regular operation, a series active power filter main circuit stops running when a loading side generates a fault of short circuit, a secondary side of the coupling transformer is of high impedance, so that current limit is realized by utilizing the parallel current limit inductor. The power electronic system not only has harmonic voltage compensating functions of the series active power filter, but also has a current limit function so as to effectively improve the power supply reliability and the power quality of a power grid, and also has remarkable economic benefit and environment-friendly benefit. The cooperative control method disclosed by the invention solves various power quality problems in the power grid, and provides theoretical and technical bases for effectively solving short circuit current limit and power quality problems of the power grid.