In the temperature range of (823–1023) K, we investigated the permeation behavior of deuterium in niobium under a pressure of (1–20) kPa and observed gradual changes in permeability and diffusivity during the permeation cycles. Notably, as the permeation cycles increased, the permeability curve exhibited an abnormal-to-normal transformation phenomenon. Increasing deuterium pressure at this stage could restore the permeability to its abnormal state. By comparing the permeation cycles of niobium foils with different oxidation degrees at 1023 K, we found that surface oxide thickness did not affect the abnormal phenomenon but reduced the diffusion coefficient of deuterium during initial permeation. Additionally, we observed that the permeation flux was proportional to the square root of pressure, indicating that diffusion still controlled permeation. After the deuterium loading, the abnormal phenomenon of the 1st permeation disappeared, and the diffusivity of deuterium in niobium decreased. The results suggested that the abnormal phenomena in 1st permeation were primarily caused by the irreversible defects resulting from the interaction between niobium and deuterium in the bulk phase and were not related to the surface effect. The pressure, concentration, and temperature of deuterium in the bulk phase accelerated the interaction between niobium and deuterium and promoted the transition of deuterium in niobium to abnormal permeation. These research findings hold significant implications for the application of niobium as a hydrogen isotope separation and purification material.