The presence of sulfur compounds in the chemical industry poses significant environmental and economic problems, including endangering human and animal lives and damaging equipment. For this purpose, hierarchical HY zeolite (Hie‐Y) with a SiO2/Al2O3 molar ratio 10 was successfully synthesized through sequential desilication‐dealumination using NH4OH treatment. A weak alkaline media with surfactant cetyltrimethylammonium bromide (CTAB) facilitates mesoporosity formation and preserves the zeolite structure. Metal oxide (CuO, MoO3) ‐ hierarchical HY zeolite nanocomposites have been prepared by one or a combination of 3 methods: 1) ion exchange, 2) precipitation, and 3) calcination. The obtained catalysts were characterized using XRD, FT‐IR, FESEM, UV‐Vis, EDS, and BET techniques. The formation of a hierarchical structure is associated with structure preservation, but partial destruction occurs based on the entering Cu in the zeolite pores. These catalysts have been studied in the oxidative desulfurization (ODS) reaction. Several parameters, including temperature, catalyst amount, DBT concentration, and reaction time, were evaluated in ODS using the Taguchi Design of Experiments. Catalytic activity order was obtained as Y<Hie‐Y<Hie‐Y/CuO<Hie‐Y/MoO3<Hie‐Y/MoO3/CuO. Results indicate an activity increase for the Hie‐Y/MoO3/CuO hierarchical structure owing to synergistic effects of secondary mesoporosity and metal oxides. The catalyst was recoverable and reused for five consecutive runs with preservation of catalytic activity.