The invention provides a servo differential compensation mechanism applied to a rotary die-cutting machine, comprising a wood board roller transmission gear driven by a main motor and a rubber cushion roller gear engaged with the wood board roller transmission gear, wherein the wood board roller transmission gear is fixedly arranged on a small-diameter shaft at the right end of a die-cutting wood board roller; and the rubber cushion roller gear is connected with a differential harmonic mechanism. The differential harmonic mechanism comprises a harmonic generator, two differential inner gears and one differential flexible gear; one differential inner gear is rigidly connected with a large gear of the rubber cushion roller to synchronously rotate, and the other differential inner gear is connected with the rubber cushion roller to synchronously rotate; the harmonic generator is connected with the flexible gear, and the flexible gear is engaged with the two differential inner gears; and a connecting shaft of the harmonic generator is connected with the harmonic generator. According to the servo differential compensation mechanism applied to the rotary die-cutting machine, provided by the invention, the diameter of the rubber cushion roller which is not ground and the data of the reduced diameter of the ground rubber cushion roller are input into a servo control computer, and a work length is compensated by a server driver, so that the size of each batch of paper boxes is ensured to be consistent after the die-cutting, the service life of a rubber cushion is prolonged and the die-cutting precision is further improved.