This paper reports a simple, one-pot, template-free synthesis of flower-like Au nanoparticles (three-dimensional branched nanoparticles with more than 10 tips) with high yield and good size monodispersity at room temperature. The size of the Au nanoflowers could be tuned by controlling the composition of the starting reaction mixture. The key synthesis strategy was to use a common Good's buffer, HEPES, as a weak reducing and particle stabilizing agent to confine the growth of the Au nanocrystals in the special reaction region of limited ligand protection (LLP). Time-course measurements by UV-vis spectroscopy and TEM were used to follow the reaction progress and the evolution of the flower-like shape. The Au nanoflowers exhibited strong surface-enhanced effects which were utilized in the design of an efficient, stable, and nontoxic Raman-active tag for in vivo applications.