The invention discloses an excitation ceiling voltage optimal configuration method and system considering difference in generator performances. The method comprises the steps that generators are grouped under anticipated faults, and the single machine equivalent of a multi-machine system is acquired to acquire an equivalent power angle curve; excitation ceiling voltage increment disturbance is carried out to calculate the regulation performance index of each generator for fault recovery of the system; the generator with the largest regulation performance index for fault recovery of the systemis selected to complete one round of configuration of the excitation ceiling voltage to determine whether the stability improvement goal of the system is reached; if the goal is reached, the configuration is ended, and otherwise whether the excitation ceiling voltage of the updated generator reaches a preset configuration upper limit by continuing to increase by a disturbance step is determined; and if the upper limit is reached, the generator which still has an excitation ceiling voltage increase margin is selected for the next round of configuration, and otherwise excitation ceiling voltageincrement disturbance is continued. According to the invention, differential configuration of the excitation ceiling voltage of the generators is realized; the transient stability of the system is better improved; and the transmission power of a regional tie line is improved.