A procedure for minimizing the environmental burden and maximizing the efficiency of storage sites used for the final disposal of spent fuel has been proposed. In this procedure, fission products (highly mobile and producing heat) are collected, and uranium and TRU-RE (transuranium-rare earth) oxide are independently stored. The possibility and applicability of radiation measurement for monitoring the nuclear materials effectively throughout the process has been simulated and evaluated. For the simulation, the properties of the chemical processes were analyzed, the major radiation emitters were determined, and the production of nuclear materials by chemical reactions were evaluated. In each process, the content of nuclear material was changed by up to 20% to represent abnormal conditions. The results showed that the plutonium peak was matched with the change in the TRU content and the measured signal was changed linearly with respect to the content change of the plutonium. From the neutron measurement, a linear response of the TRU content variation was obtained. In addition, a logic diagram was developed for the nuclear monitoring. The integration of radiation detections is recommended for monitoring the process effectively and efficiently.