A highly shape-selective H[Zn,Al]ZSM-5/SiO2 composite catalyst was prepared by direct incorporating Zn species via isomorphous substitution into the zeolite framework and subsequent SiO2 deposition on zeolite surface. Its catalytic performance in methanol to aromatics (MTA) was compared with Zn/HZSM-5/SiO2 prepared by impregnation of Zn species and subsequent SiO2 deposition. The textural properties and acidic properties as well as the subsequent catalytic performances of the resultant catalysts in MTA reaction were obviously influenced by the introduction method of Zn species. H[Zn,Al]ZSM-5/SiO2 prepared by isomorphous substitution contained more inter-crystalline voids, which provided much space to resist deposition of coke and avoided quick blockage of micropore entrances. In contrast, Zn/HZSM-5/SiO2 prepared by impregnation contained sub-nanometric ZnO clusters at the pore entrances, which might restrict large molecule products diffusion and deteriorated the catalyst deactivation. Moreover, the sum of strong and medium acid sites in H[Zn,Al]ZSM-5/SiO2 was more than that in Zn/HZSM-5/SiO2, which meant there were more active sites for cyclization and aromatization steps in MTA reaction in the former. As a result, the lifetime of H[Zn,Al]ZSM-5/SiO2 was almost twice that of Zn/HZSM-5/SiO2. In addition, the enhancement in catalytic activity by Zn introduction and the improvement in para-selectivity in xylene by SiO2 deposition were also studied. Finally, nearly 100% methanol conversion, 95.6% para-selectivity in xylene and 18.2% para-xylene yield were simultaneously obtained over the stable H[Zn,Al]ZSM-5/SiO2 (with 24 h lifetime) in MTA reaction.