The invention discloses a method and a system of equivalent impedance compensation. The method includes that a reference module and an adjustable module receive externally exerted stimulation disturbance sources; the reference module presets performance indexes according to states or outputs of the reference module, and the adjustable module measures adjustable performance indexes of the reference module; the preset performance indexes are compared with the adjustable performance indexes to obtain parameter difference vectors; whether the parameter difference vectors fluctuate within a preset range is judged; if yes, modified impedance parameters are output; if no, parameter initial value setting for a parameter self-adaptive control module is achieved, and the parameter difference vectors are input to the parameter self-adaptive control module; and the parameter self-adaptive control module adopts self-adaptive ratios to achieve compensation for the adjustable performance indexes and equivalent impedance. The invention provides a compensation algorithm of the equivalent impedance based on the model reference self-adaptive principle, and the algorithm distinguishes impedance parameters of a permanent magnet motor in a wind power plant equivalent model according to the model reference self-adaptive principle to improve precision of an equivalent algorithm.