Micro-mesoporous Beta-FDU-12 (BF) materials were synthesized by a nano-assembling method with different amounts of microporous Beta materials. CoMo catalysts, with Co and Mo active metals supported on BFA composites (a mixture of BF and gamma-Al2O3), were prepared by two-step incipient-wetness impregnation procedures. The BF micro/mesoporous materials and their corresponding CoMo/BFA catalysts were characterized by various techniques, including small-angle X-ray scattering (SAXS), X-ray diffraction(XRD), transmission electron microscopy (TEM), Fourier Transform Infrared(FTIR), pyridine-FTIR, nitrogen adsorption-desorption, UV-vis diffuse reflectance spectroscopy (DRS), Raman and X-ray photoelectron spectroscopy(XPS). The characterization results indicated that BF micro/mesoporous materials had the structures with both of the mesoporous FDU-12 materials and microporous Beta materials. Among the catalysts with different mass ratios of Beta/F127, CoMo/BFA2 catalyst showed the best comprehensive hydrofining performance with a hydrodesulfurization (HDS) efficiency of 98.1% and a hydrodenitrogenation (HDN) efficiency of 95.6% for FCC diesel, which was ascribed to the appropriately synergistic effect of pore properties and acid property. Furthermore, after the modification of ethylenediaminetetraacetic acid (EDTA) by the post-treatment method, the dispersibility of Mo species on the catalyst surface was significantly improved, which led to a better hydro-upgrading performance of FCC distillates, whereas gasoline desulfurization efficiency of 94.2% and octane loss of 0.8 units, and diesel desulfurization efficiency of 99.0% and denitrification efficiency of 97.3%.