The self-assembly of nanoparticles to hierarchal structures receives increasing concern nowadays. In this paper, we report hierarchal silica clusters composed of multi-lamellar silica vesicles (MSVCs) through self-assembly and mineralization. Herein, an amphiphilic comb-like polymer with a siloxane skeleton and Pluronic P123 were introduced as the co-template, and tetraethoxysilane (TEOS) was the silica source. The flexible templates and gradually solidified silica shell provided the vesicles with proper hardness to adapt to the shape change during the aggregation and fusion, and the morphology of the MSVCs was fixed by silica finally. The obtained MSVCs were 400–700 nm in dimension, and composed of several multi-lamellar silica vesicles with ca. 105–130 nm in size, respectively. The effect of template ratio, pH value and temperature were discussed to illustrate the proper conditions for preparing hierarchal MSVCs, and the formation of MSVCs was discussed based on time-dependent observations.