Uranium and plutonium are required to be accounted in spent fuel head-end and major recovery area in pyro-process for safeguards purpose. The possibility of neutron resonance technique, as a non-destructive analysis, was simulated on isotopic fissile analysis for large scale process. Neutron resonance technique has advantage to distinguish uranium from plutonium directly in mixture. Simulation was performed on U235 and Pu239 assay in spent fuel and for scoping examination of assembly type. The resonance energies were determined for U235 and Pu239. The linearity in the neutron transmission was examined for the selected resonance energies. In addition, the limit for detection was examined by changing sample density, thickness and content for actual application. Several factors were proposed for neutron production and the moderated neutron source was simulated for effective and efficient transmission measurement. From the simulation results, neutron resonance technique is promising to analyze U235 and Pu239 for spent fuel assembly. An accurate fissile assay will contribute to an increased safeguards for the pyro-processing system and international credibility on the reuse of fissile materials in the fuel cycle.