The twin boundaries and inherent lattice strain of five-fold twin (5-FT) structures offer a promising and innovative approach to tune nanocrystal configurations and properties, enriching nanomaterial performance. However, a comprehensive understanding of the nonclassical growth models governing 5-FT nanocrystals remains elusive, largely due to the constraints of their small thermodynamically stable size and complex twin configurations. Here, we conducted in situ investigations to elucidate the atomic-scale mechanisms driving size-dependent and twin configuration-related aggregation phenomena between 5-FT and other nanoparticles at the atomic scale. Our results reveal that surface diffusion significantly shapes the morphology of aggregated nanoparticles, promoting the symmetrical formation of 5-FT, especially in smaller nanoparticles. Moreover, the inherent structural characteristics of 5-FT mitigate the dominance of surface diffusion in its morphological evolution, retarding the aggregation evolution process and fostering intricate twin structures. These findings contribute to advancing our capacity to manipulate the configuration of twinned particles, enabling more predictable synthesis of functional nanomaterials for advanced engineering applications.