Herein, two atomically precise silver nanoclusters, Ag54 and Ag33, directed by inner anion templates (CrO42‐ and/or Cl‐), are initially isolated as a mixed phase from identical reactants across a wide temperature range (20‐80 °C). Interestingly, fine‐tuning the reaction temperature can realize pure phase synthesis of the two nanoclusters; that is, a metastable Ag54 is kinetically formed at a low temperature (20 °C), whereas such a system is steered towards a thermodynamically stable Ag33 at a relatively high temperature (80 °C). Electrospray ionization mass spectrometry illustrates that the stability of Ag33 is superior to that of Ag54, which is further supported by density functional theory calculations. Importantly, the difference in structural stability can influence the pathway of 1,4‐bis(pyrid‐4‐yl)benzene induced transformation reaction starting from Ag54 and Ag33. The former undergoes a dramatic breakage‐reorganization process to form an Ag31 dimer (Ag31), while the same product can be also achieved from the latter following a noninvasive ligand exchange process. Both the Ag54 and Ag33 have the potential for further remote laser ignition applications. This work not only demonstrates how temperature controls the isolation of a specific phase, but also sheds light on the structural transformation pathway of nanoclusters with different stability.