The invention relates to a multi-micro network distributed harmonic compensation method. The method comprises steps that a mathematical model of primary control is established; a primary voltage controller is designed, and a control object and a weighting function are taken as generalized controlled objects to construct an optimization problem model for the generalized controlled objects; a quasi-proportional resonant controller is designed; a three-phase voltage at a common coupling point is acquired, a harmonic distortion rate is calculated, secondary control is performed to generate a control signal based on the harmonic distortion rate, and the control signal is transmitted to primary control to achieve harmonic suppression. The method is advantaged in that primary control enables theoutput voltage to be robust, the harmonic distortion rate of the common coupling point is controlled through secondary control by transmitting the compensation signal to primary control, and the output voltage can be made to have stronger robustness and better harmonic suppression capability.