Zeolitic imidazolate frameworks (ZIFs)-based catalysts with a high surface area and structural features have received great attention for potential use in complete eliminating refractory thiophenic toxic compounds from liquid fuels. In this paper, composite frameworks of Co/Zn-based ZIFs@TiO2 were synthesized and their catalytic ability for deep oxidative desulfurization (ODS) of dibenzothiophene (DBT) was examined. The main aim of this study is investigation the effects of Zn2+ and Co2+ ion centers in ZIF-8 and ZIF-67 frameworks on the coordination with TiO2 nano particles and eventually on the catalyst performance. The obtained results verified that the intensity of the N-Ti-O bond was influenced by the particle size of the ZIF crystals as well as the type of metal centers (Zn or Co). Over the small size ZIF-8-M particles, the aggregation of TiO2 layer decreased the intensity of N-Ti-O bonds. Meanwhile, the lower energy of Zn-N bond and controlled particle size of ZIF-8-W were favorable for partially replacing Zn2+ with Ti4+ and forming extra N-Ti-O species which are supposed to enrich active Ti-peroxo intermediates for the ODS progress. In the case of ZIF-67, unsaturated Co-N bonds further improved DBT uptake. The maximum efficiency of 98.6% for DBT removal was achieved using ZIF-8-W@TiO2 due to the high surface area (SBET=1548 m2/g), uniform TiO2 distribution, and further N-Ti-O bonds. The recyclability investigation also verified good stability for the proposed composite catalyst.