The unique 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, due to constraints imposed by small thermodynamically stable size and complex twin configurations, gaps persist in understanding the nonclassical growth models of 5-FT nanoparticles. Here, we in-situ investigated the mechanisms underlying size-dependent and twin configuration-related aggregation growth phenomena between 5-FT and other nanoparticles at the atomic scale. The results find that surface diffusion shapes the morphology of aggregated nanoparticles, promoting symmetrical 5-FT formation, particularly involving smaller nanoparticles. Additionally, the inherent structure of 5-FT mitigates the dominance of surface diffusion in its morphological evolution, retarding the aggregation evolution process and fostering intricate twin structures. Our findings contribute to advancing our ability to manipulate the configuration of twinned particles and achieve a more predictable synthesis of novel functional nanomaterials for engineering applications.