Inferior diffusion capacity and insufficient acid density hinder the practical application of ZSM-48 zeolite. Finding a simple and practical strategy to simultaneously address these two defects remains a challenge. In response to this dilemma, we developed an unconventional seed-assisted synthesis strategy for Al-rich hierarchical ZSM-48 zeolite. This approach allows for achieving a broader range of silica to alumina ratio and accelerates the entire crystallization process through the selection of unconventional seeds. The synergy between the seed and organic template was demonstrated to play a pivotal role in facilitating nucleation. Direct evidence from 1H-29Si CP MAS NMR, TG, and IR results demonstrates that hexamethonium ions (HM2+) electrostatically adsorb at the defect sites on the seed, thereby promoting nucleation sites formation. Smaller seed crystals undergo more etching during the induction period, resulting in additional defects and enhanced nucleation ability. The obtained catalyst exhibits a diffusion time constant (Deff/L2) nine times that of conventional ZSM-48 zeolite when using p-xylene as a probe molecule. In m-xylene isomerization reaction, Al-rich hierarchical ZSM-48 demonstrates excellent stability along with higher selectivity and yield for p-xylene compared to typical ZSM-5 catalysts. Remarkably, long-term testing of 1000 h yields over 22.5 % of p-xylene, indicating the potential of this catalyst as an alternative for xylene isomerization reaction. This work not only advances the practical application process of ZSM-48 catalyst but also provides valuable insights for optimizing other zeolites.