Knowledge of the molecular formation mechanism of metal nanoclusters is essential for developing chemistry for accurate control over their synthesis. Herein, the "top-down" synthetic process of monodisperse Au13 nanoclusters via HCl etching of polydisperse Aun clusters (15 ≤ n ≤ 65) is traced by a combination of in situ X-ray/UV-vis absorption spectroscopy and time-dependent mass spectrometry. It is revealed experimentally that the HCl-induced synthesis of Au13 is achieved by accurately controlling the etching process with two distinctive steps, in sharp contrast to the traditional thiol-etching mechanism through release of the Au(i) complex. The first step involves the direct fragmentation of the initial larger Aun clusters into metastable intermediate Au8-Au13 smaller clusters. This is a critical step, which allows for the secondary size-growth step of the intermediates toward the atomically monodisperse Au13 clusters via incorporating the reactive Au(i)-Cl species in the solution. Such a secondary-growth pathway is further confirmed by the successful growth of Au13 through reaction of isolated Au11 clusters with AuClPPh3 in the HCl environment. This work addresses the importance of reaction intermediates in guiding the way towards controllable synthesis of metal nanoclusters.