The structural transformation of high-nuclearity silver clusters from one to another induced by specific stimuli is of scientific significance in terms of both cluster synthesis and reactivity. Herein, we report two silver-thiolate clusters, [Mo6O22@Ag44] and [Mo8O28@Ag50], which are templated by isopolymolybdates inside and covered by iPrS- and PhCOO- ligands on the surfaces. Amazingly, the [Mo8O28@Ag50] can be transformed from [Mo6O22@Ag44] by adding PhCOOH which increases the degree of condensation of molybdates template from Mo6O228- to Mo8O288-, then enlarging the outer silver shell from Ag44 to Ag50. The evolution of solution species revealed by time-dependent electrospray ionization mass spectrometry (ESI-MS) suggests a breakage-growth-reassembly (BGR) transformation mechanism. These results not only provide a combined assembly strategy (anion-template + induced transformation) for the synthesis of silver-thiolate clusters but also help us to better understand the complex transformation process underpinning the assembly system.