Detailed mechanistic investigations of the interrelated roles of multiple key structure‐directing agents in the growth solution of Au nanoparticles (AuNPs) is required for the optimization of synthetic protocols. Here, we report a robust seed‐mediated growth strategy for synthesizing multibranched NPs (MB‐AuNPs) with monodispersed size distribution, and investigate the roles of Ag ions and 4‐(2‐hydroxyethyl)piperazine‐1‐ethanesulfonic acid (HEPES) based on an overgrowth synthesis approach. The intertwining roles of Ag+, surface‐capping stabilizers, and reducing agents were elucidated, and used to control the morphology of MB‐AuNPs. The overgrowth of MB‐AuNPs involves two distinct underlying pathways, namely, directional and anisotropic growth of Au branches on specific facets of Au seeds as well as an aggregation and growth mechanism governed by HEPES. In addition to Ag ions and HEPES, morphology tunability can also be achieved by pre‐modification of the Au seeds with molecular probes. Optimized probe‐containing MB‐AuNPs prove to be excellent surface‐enhanced Raman scattering (SERS) substrates and nanozymes. Taken together, the results of this work reveal the mechanistic evolution of nanocrystal growth which should stimulate the development of new synthetic strategies, improve the capabilities of tuning the optical, catalytic, and electronic properties of NPs, and further advance their applications in biolabeling, imaging, biosensing, and therapy.