Superconducting magnet power of stabilized intense magnetic fields adopts double-inverse-star silicon controlled rectifying technology; it is a typical non-linear load, which will bring about larger idle impact and harmonic pollution at runtime. Aiming at the program planning for chained high-voltage active power filter system in scientific devices, combing with the non-linear characteristics of active power filter system, a method adopting the fractional-order PI controller instead of ordinary PI controller is proposed to realize inner loop decoupling, and based on improved Oustaloup algorithm to achieve solution of fractional calculus. Through simulation and experimental comparison, the running effect of fractional-order PI controller and conventional PI controller is analyzed. According to simulation and experiment, this fractional-order PI controller is correct, and has a certain value for reference.