The atomic-scale defects such as (deuterium, helium)-vacancy clusters in nuclear energy materials are one of the causes for the deterioration of the macroscopic properties of materials. Unfortunately, they cannot be observed by transmission electron microscopy (TEM) before they grow to the nanometer scale. Positron annihilation spectroscopy (PAS) has been proven to be sensitive to open-volume defects, and could characterize the evolution of the size and concentration of the vacancy-like nanoclusters. We have investigated the effects of He-D interaction on the formation of nanoscale cavities in Fe9Cr alloys by PAS and TEM. The results show that small-sized bubbles are formed in the specimen irradiated with 5 × 1016 He+/cm2, and the subsequent implanted D-ions contribute to the growth of these helium bubbles. The most likely reason is that helium bubbles previously formed in the sample captured deuterium injected later, causing bubbles to grow. In the lower dose He-irradiated samples, a large number of small dislocations and vacancies are generated and form helium-vacancy clusters with the helium atoms.