Using CTAB as the mesostructure directing agent, a novel micro/mesoporous composite material of Beta-MCM-48 was synthesized and self-assembled from nanocrystal Beta solutions by two-step hydrothermal method in this study. The typical physico-chemical properties of material were characterized by the techniques and measurements of BET surface area, pore volume, pore size, XRD and TEM. Based on the characterization results, it could be found that BM48 composite simultaneously possessed BEA microporous structure and cubic Ia3d mesoporous structure, and the degree of mesoporous order was comparably uniform, which construct a suitable gradient of micro/mesopore structures and facilitated the diffusion of large size reactant molecules. The HDS performance in a microreactor indicated that NiMo/ABM48 series catalysts with different BM48 contents and various Mo loadings showed better hydrodesulfurization performances compared with the conventional NiMo/Al2O3 catalyst, and the optimal content of BM48 in the supports was 20 m%, and the suitable loading of Mo in the catalyst was 15 m%. The best HDS efficiency reached 98.3% and the corresponding sulfur content in product was 23.02 µg•g-1, which met the sulfur regulation of Euro IV ultra clean diesel specification.