The invention relates to an instantaneous power factor compensation control method and system. Current of a three-phase system and current of a compensation device are collected in real time, and three phases of load currents are obtained; the load currents are decomposed into an active current component and a reactive current component, and an load instantaneous power factor PFL is calculated; and an amplitude Iqref of a reactive control amount and an instant value iqref of a three-phase reactive control amount are calculated according to a given target power factor PFref and the load instantaneous power factor, and the instant value of the three-phase reactive control amount serves as an instant value of a three-phase current compensation control instruction of the compensation device. According to the invention, the instant active current component and the reactive current component of the load are calculated in real time to obtain the instant power factor of the load, the problem that an original algorithm is low in instantaneity and low in response speed when being used to track a rapidly changed load is solved, a power factor control unit is used to calculate the instantaneous power factor control amount directly, and the problem that a PI regulation is low in instantaneity in an original method is solved.