Palladium coated niobium foil (Pd-Nb-Pd) is widely used as the hydrogen and deuterium-permeable materials for both the hydrogen purification and the hydrogen pumping. However, the performance of Pd-Nb-Pd membranes is usually affected by the degassing treatment (DT) that is typically implemented during the permeation test. In this paper, effects of DT on the deuterium permeability of the Pd-Nb-Pd composite membranes are investigated with varying degassing time. The deuterium permeability test is performed in the temperature range of 573–723K at the driving pressures of 1–5kPa. Results show that the permeation behavior of Pd-Nb-Pd membranes is affected by DT at 673K during deuterium permeation. With the increasing DT time, the permeation performance deceases. The deuterium permeability of the sample heated at 723K is 1.23×10−7molm−1·s−1·Pa−0.5 at the 10min DT time, one order of magnitude higher than 5.33×10−8molm−1·s−1·Pa−0.5 of the sample at the 60min DT time. The corresponding apparent activation energies are 20.11kJ/mol and 52.55kJ/mol for the samples at 10min and 60min DT time, respectively. Scanning electron microscope and Auger electron spectroscopy analysis reveal that a large number of pores are formed in the top Pd coating layer, and the inter-diffusion at the Pd-Nb interface occurs during the permeation experiment. Therefore, it is suggested that both the surface microstructure change and the inter-diffusion are attributed to the decline of deuterium permeability.