The invention discloses a multilayer film registration control system and method for flexible RFID tag coiling recombination, and the method comprises the steps: (a), forming the system through a feeding unit, a recombination unit, and a material receiving unit; (b), inputting technological reference values: tag step, working tension and tension boundary; (c), enabling a plurality of sensors to cooperatively detect the registration deviation of a multilayer film in a movement feeding direction according to the triggering position relation, building a tension and registration deviation relation model, and converting the registration deviation into a tension adjustment variable; (d), synchronizing the feeding speed of the multilayer film under the target tension in a mode of tension-position-speed closed loop control, correcting the registration deviation, and carrying out the recombination; (e), building a feeding and material receiving coiling diameter algorithm, adjusting the torque output of a driver according to the changes of a coiling diameter, and guaranteeing the constant-tension operation of material feeding and receiving. The method can achieve the high-speed and high-precision registration requirements of the multilayer film under the condition of a controllable tension, and is especially suitable for the preparation of a flexible RFID tag recombination product.