This article is intended to deepen the understanding of molecular shape selectivity of HZSM-5 in catalytic conversion of biomass pyrolysis vapors through the study of catalyst effective pore size. Ex-situ catalytic fast pyrolysis (CFP) of biomass over HZSM-5 with varied catalyst loadings were carried out using a continuous feeding two-stage fluidized-bed/fixed-bed combination reactor. Results showed that in addition to the shape selective reactions inside catalyst channels, cracking and aggregating reactions occur at the external surface of HZSM-5. The catalytic activity of HZSM-5 external surface for some heavy compounds was observed to be relatively low. On the basis of the molecular dimension information provided by quantum chemical calculations, it was found that HZSM-5 has an effective pore size which is significantly larger than its static pore size at CFP temperature. Catalytic alkylation of naphthalene with methanol over HZSM-5, HZSM-5@silicalite-1, HSAPO-34, HM, Hβ, HUSY and HMCM-41 were further compared to determine the effective pore size of HZSM-5. It is proposed that the effective pore size of HZSM-5 at CFP temperature is between the critical molecular diameters of 2,3- and 1,6-dimethylnaphthalene (between 7.520 and 7.961 Å).