Due to continuous self-sealing and good mechanical properties, the Tamusu clay rock of Inner Mongolia has been identified as the pre-selected site for high-level radioactive waste geological disposal site in China. The study of chemical behaviors related to Tamusu clay rock, such as nuclide migration, will be an important content of the performance assessment and safety assessment of the disposal repository in the future. The diffusion behavior of HTO and Se(IV)/Se(VI) with different compacted column lengths in Tamusu clay rock is discussed by the through-diffusion method. The diffusion coefficient, rock capacity factor, effective porosity, and other diffusion parameters closely related to nuclide migration are calculated, and the mechanism of nuclide diffusion is preliminarily discussed. The results show that D a (6.23 × 10−11∼17.96 × 10−11 m2 s−1), D e (1.62 × 10−11∼4.67 × 10−11 m2 s−1) for HTO increase with the increase of the compacted column length, and it is proposed that the diffusion process of HTO is affected by the change of geometrical factor and path tortuosity. D a (7.29 × 10−13∼1.74 × 10−13 m2 s−1), D e (5.15 × 10−12∼2.15 × 10−12 m2 s−1) for Se(IV), D a (3.11 × 10−12∼1.09 × 10−12 m2 s−1), D e (2.53 × 10−12∼1.09 × 10−12 m2 s−1) for Se(VI), which decrease with the increase of the compacted column length, it is mainly due to the existence of anion repulsion effect.