A unique hierarchical TS-1/FDU-12 (TF) micro-mesoporous composite was synthesized by nano-assembly method, and was used as an excellent support for high-efficiency hydrodesulfurization (HDS) catalyst (NiMo/TF) of dibenzothiophene (DBT). The introduction of TS-1 nanocrystals provided more S vacancies and more acidic sites to the NiMo/TF catalysts, and showed no effect on the highly ordered three-dimensional structure of the composites, leading to excellent HDS performance of NiMo/TF catalysts. The superior acidity of NiMo/TF favored the HYD pathway of DBT, resulting in improved DBT HDS activity with up to 98.0 % desulfurization degree. In addition, NiMo/TF presented an optimal reaction rate constant (kHDS) of 5.9 × 10-4 mol g-1 h−1, a turnover frequency (TOF) value of 1.6 h−1 and a low activation energy (Ea) of 47.7 kJ mol−1, which are due to the synergistic effect of large specific surface area, appropriate pore size, abundant Brønsted & Lewis acidic sites, suitable MSI, high sulfurization degree and highly dispersed MoS2 active phases.