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Subsynchronous oscillation (SSO) fault can cause torsional vibration and fatigue damage of the shafting system, thereby endanger the safe operation of the turbo-generator set. A novel framework for the online evaluation of shaft fatigue damage suffered from SSO is proposed in this paper. The main ingredients of the framework are a calculation method of the turbo-generator shaft torque, rain-flow counting method, S-N curves and linear damage accumulation law. The shaft torque calculation method, based on the measured torsional angle and generator voltage and current data, is mainly discussed. The effects of damping and electromechanical coupling under complex operating conditions are included in the measured data, and the calculated results of the torque are accurate. The novel framework was used to evaluate the fatigue damage of a 1000 MW turbo-generator shaft that suffered an actual SSO fault caused by a high-voltage direct current (HVDC) transmission system and some meaningful conclusions were given.