The separation performance of tritium by the thermal diffusion method with low inventory was simulated as an alternative method to the cryogenic distillation in Fusion Fuel Cycle. The separation performance of thermal diffusion method was evaluated by the ternary transport equations with isotope exchange reaction. The results for HT - H2 system, show the isotope exchange reaction, H2 + T2 = 2HT, plays an important role in the separation performance of tritium, even in a tracer level of tritium.