The invention provides a method and system for suppressing subsynchronous resonance of a compensated transmission system. The method includes: collecting rotor-side three-phase current Irabc, stator-side three-phase current Isabc and stator-side three-phase voltage Usabc of a grid-side converter of a double-feed fan of the compensated transmission system; subjecting Irabc, Usabc and Isabc to Clarke transmission to acquire rotor-side current Irabeta, stator-side current Isabeta and staor-side Usabeta under two-phase stationary coordinates; according to a rotor current reference value Irabeta<*> and Irabeta, acquiring a first feedforward control component; calculating a second feedforward control component according to equivalent reactance parameters, leakage coefficients and Irabeta of the rotator side; according to equivalent reactance parameters of the stator side, common reactance of the stator side and the rotor side and Isabeta and Usabeta, calculating flux control components of the stator side; according to the first feedforward control component, the second feedforward control component and flux control components, calculating control voltage Urabeta<*> of the rotor side; performing space vector modulation on Urabeta<*> to acquire switching control signals of the grid-side converter to suppress the subsynchronous resonance of the compensated transmission system.