The size uniformity and spatial dispersion of nanoparticles (NPs) formed by ion implantation must be further improved due to the characteristics of the ion implantation method. Therefore, specific swift heavy ion irradiation and thermal annealing are combined in this work to regulate the size and spatial distributions of embedded Au NPs formed within LiTaO3 crystals. Experimental results show that small NPs migrate to deeper depths induced by 656 MeV Xe35+ ion irradiation. During thermal annealing, the growth of large Au NPs is limited due to the reductions in the number of small Au NPs, and the migrated Au NPs aggregate at deeper depths, resulting in a more uniform size distribution and an increased spatial distribution of Au NPs. The present work presents a novel method to modify the size and spatial distributions of embedded NPs.