ZSM-5-MCM-41 composite molecular sieve with strong acidity and different Si/Al molar ratios (denoted as ZMC-M(x), M=1.5，2.0 and 2.5 mol/L NaOH respectively, where x represented the SiO2/Al2O3 molar ratios of the mother liquid) were successfully synthesized by assembling zeolite subunits, which generated by hydrolysis of ZSM-5 in a NaOH aqueous solution using cetrimonium bromide as a template. And then MoS2/ZMC and Ni-MoS2/ZMC catalysts were prepared by impregnation method. Different NaOH treatment concentrations were examined to determine the optimum alkali treatment concentration. The effects of Si/Al molar ratio and NiMo bimetallic sulphides on the hydrodesulfurization of thiophene were also investigated using thiophene /n- tetradecane as the model compound. The results showed that with concentration of NaOH increasing the ZMC composite molecular sieve formed more mesoporous phase. However, the high concentration of NaOH treatment destroyed the structure of ZSM-5. Therefore, the optimal NaOH concentration was 2.0 mol /L. With the increase of Si/Al ratio of ZMC, the activity of hydrodesulfurization increases. Moreover, the hydrodesulfurization performance of the composite molecular sieve supported NiMo bimetallic sulfide is better than that of the composite molecular sieve supported MoS2. Under the conditions of H2 pressure of 3 MPa, temperature of 280 ºC and 40 ml (1000 ug/L) thiophene/n-tetradecane, 20%MoS2/ZMC-2.0 (70) and 20%Ni-MoS2/ZMC-2.0 (70) catalysts for the thiophene conversion rate of hydrodesulfurization rate reached 84.1% and 95.2% respectively.