The synthesis of mesoporous zeolites has garnered attention with regard to improving their catalytic and adsorption performances. While the hard-templating method provides opportunities to design precisely controlled hierarchical micro- and mesoporous structures, synthesizing mesoporous zeolites without external precipitation requires significant work. This is mainly due to the absence of usable templates other than carbon with hydrophobic surfaces. Herein, it is demonstrated that the Co3O4 template is valuable in preparing mesoporous silicalite-1 and ZSM-5 with a precisely controlled porous structure through hydrothermal synthesis. Unlike conventional carbon templates, the Co3O4 template is relatively hydrophilic, effective in suppressing external precipitation, and is reusable by dissolving in an acidic solution. The crystallization process also differs from that of the carbon template, as the silicate precipitates on a 3D ordered nanoporous Co3O4 scaffold, followed by crystallization and crystal growth. Furthermore, it is unexpectedly observed that the zeolite crystallization is accelerated in the Co3O4 template. The synthetic approach utilizing nanoporous metal oxides opens new doors for the control of the hierarchical structure of zeolites, as well as for the design of metal oxide-zeolite nanocomposite catalysts, due to the potential extensibility of the combination of metal oxides and zeolites.