The invention belongs to the field of nuclear radiation, and particularly relates to a method for producing carrier-free < 99 > Mo by a heavy water reactor. At present, global < 99 > Mo is mainly carrier-free < 99 > Mo produced by a research reactor through fission, production of carrier < 99 > Mo by using a heavy water reactor has been developed and utilized internationally, and an example for producing carrier-free < 99 > Mo by using a commercial heavy water reactor has not been seen up to now. By means of the method, large-scale stable production and supply of < 99 > Mo are achieved through the heavy water reactor, and the produced < 99 > Mo is mainly applied to the field of nuclear medicine diagnosis. The method comprises the following steps: 1, confirming loading conditions; 2, determining a loading position; 3, the target piece is put into a pile; step 4, carrying out in-pile irradiation; and 5, discharging the target from the reactor core. On the premise that safe operation of the reactor is not affected and fuel loss is reduced as much as possible, the carrier-free < 99 > Mo is produced through irradiation of the heavy water reactor, and the requirement of the nuclear medicine field for < 99 > Mo is met.