The tritium plant needs to recover unburned deuterium and tritium for recycling to achieve tritium self-sufficiency. The tritium recovered by the water detritiation system (WDS) contains a large amount of protium. High purity deuterium (D) and tritium (T) are required as fuel for fusion reactor while hydrogen (H) always exists as an impurity of the fuel. Therefore, a hydrogen isotope separation system (ISS) is essential for fuel cycle in fusion reactor. ISS separates the recovered H, D, T, and removes the impurity protium (H) to obtain high-purity fuel deuterium and tritium. In this paper, two hydrogen isotope separation systems for the inner fuel cycle system and the outer fuel cycle system of CFETR (China Fusion Engineering Test Reactor) are respectively established according to the disparity in tritium concentration of hydrogen isotopes gas. The tritium inventory in the ISS is expected to be very large, evaluating the tritium inventory of ISS facilitates the evaluation of the minimum initial startup tritium inventory for the operation of the fusion reactor. The chemical simulation software Aspen Plus is used to simulate the separation process of ISS. The purity of products and the distribution of hydrogen isotopes in each distillation column are obtained. Based on the simulated data, the tritium inventory in each distillation column is calculated.