The EMT, EMT/FAU intergrowths and FAU zeolites were synthesized and applied as the additives of the catalysts for FCC gasoline hydro-upgrading. The physico-chemical properties of the as-synthesized catalysts were characterized by various techniques including XRD, N2 adsorption–desorption, HRTEM, SEM, etc. The results revealed that the zeolite-incorporated catalysts exhibited high specific surface areas, pore volumes and suitable acidities. Among the supported CoMo catalysts containing pure EMT zeolite with different particle sizes, the micrometer-sized EMT-incorporated catalyst CoMo/AE-3 showed the highest HDS efficiency (96.1%), but with the greatest loss of octane number (2.3 unit) due to its excessive olefin saturation. Moreover, compared with the supported CoMo catalysts containing micrometer-sized EMT and EMT/FAU intergrowth zeolites, the EMT/FAU-incorporated catalyst CoMo/AE-5 (CoMo/EMT/FAU-2-γ-Al2O3) with excellent pore structure and suitable amounts of B and L acidity sites exhibited a good balance in HDS efficiency (94.6%) and RON preservation (0.5 unit). This could be ascribed to the synergy of zeolite EMT and zeolite FAU that balanced the functions among the HDS, aromatization and isomerization.