Deep hydrogenation of polycyclic aromatic hydrocarbons (PAHs) into jet fuel is an important strategy for the upgrading of light cycle oil (LCO). Zeolite-supported metal catalysts have exhibited good catalytic performance for hydrogenation of PAHs under relatively mild conditions. However, the impacts of acidity variations in zeolite supports, arising from the differences in framework Al (AlF) distribution on the catalytic behavior of zeolite-supported metal catalysts in the deep hydrogenation of PAHs remains unclear. Herein, two series of mesoporous ZSM-5 samples, that is ZSM-5-E-x and ZSM-5-F-x, with the differences in AlF distribution but similar Si/Al ratios, were prepared in the crystallization system with or without NaOH. The results of NH3-TPD, Pyridine-IR, N2 adsorption-desorption and SEM reveal that two series of HZSM-5 samples have similar acid density and acid strength, textural properties, morphology and particle size. However, the results of XPS, 27Al MAS NMR, 2,6-Ditert-butylpyridine-IR, catalytic cracking of 1,3,5-triisopropylbenzene and the controlled reactions as well as DFT calculation indicate that the higher enrichment degree of AlF on the external surface and the suitable arrangement mode of AlF in ten-membered ring (10-MR) of HZSM-5-F-x compared to HZSM-5-E-x in case of the similar Si/Al ratios, result in Pt/HZSM-5-F-x exhibiting remarkably-improved deep hydrogenation performance of phenanthrene (PHE) compared to Pt/HZSM-5-E-x. Particularly, the selectivity to perhydrophenanthrene (PHP) over Pt/HZSM-5-F-50 can reach above 99.0% at a conversion of PHE (>99.0%). Furthermore, Pt/HZSM-5-F-50 exhibits well reusability. This work helps to clarify the impact of AlF distribution in ZSM-5 on catalytic hydrogenation performance for PAHs, providing valuable guidance for design and development of efficient catalysts for the hydrogenation of PAHs.