Framework aluminum (Al-F) has a correlative relationship with the acid sites in a zeolite, which has been regarded as the key point during the adsorption behavior in alkylation of benzene with methanol. Here, the Al-F distribution in HZSM-5 channels was successfully controlled by different pore-filling agents and organic structure-directing agents (OSDAs) in the synthesis step. HZSM-5 samples with Al-F preferentially located in the intersections and sinusoidal/straight channels were synthesized using tetrapropylammonium hydroxide and pentaerythritol with Na cations as an OSDA and a pore-filling agent, respectively. Catalytic performances in alkylation of benzene with methanol showed that HZSM-5 zeolite with Al-F sitting in the channel and channel intersections generated a coadsorption effect yielding higher benzene conversion, xylene selectivity, and catalytic stability in this reaction. Meanwhile, HZSM-5 zeolite with more Al-F located particularly in the sinusoidal channel exhibited better shape selectivity to the para-xylene product.