ZSM-48 is a unidimensional zeolite that is frequently used as acid component of bi-functional hydroisomerization catalyst. As selectivity towards unwanted cracking products increases with retention time of isomerized products inside micropores, shortening their retention time inside the micropores by reducing channel length offers an effective way to improve isomerization selectivity. Direct synthesis of unidimensional zeolitic crystals with reduced channel axis is particularly difficult, since they habitually grow into rod-like shape along their channel direction. Post-synthetic bead-milling is a cost effective, mechanochemical method to decrease crystal size of zeolites from micro meter to nano meter scale, but suffers from amorphization or partial destruction of zeolitic crystals. Consequently, a post-milling recrystallization process is often entailed to remedy the destructed domains, which, nonetheless, readily causes secondary crystal growth and formation of bulky crystals that compromises the effect of bead-milling. Here, we show that porogen-assisted recrystallization can overcome the problem to fabricate channel axis reduced ZSM-48 nanocrystals. The Si/Al ratio is tunable between 30 and 200 and the acidity is largely preserved after recrystallization. The catalytic advantages of the obtained material are demonstrated in catalytic n-heptane hydroisomerization. The obtained ZSM-48 nanocrystal with Si/Al ratio of 100 outperforms the rest samples and shows enhanced isomerization yield (72% vs 62%) with respect to the parent sample. By combined diagnoses of the impact of diffusion length on product selectivity (product shape selectivity) and kinetic studies, selectivities to monomethyl branched isomers (2-methyl hexane and 3-methyl hexane) and small bulky dimethyl branched isomers (2,3- and 2,4-dimethyl pentane) are attributed to product shape selectivity, whereas the formation to bulky dimethyl branched isomers (2,2- and 3,3-dimethyl pentane) is hindered mainly by transition-state shape selectivity. The combined destructive-constructive synthetic protocol and the revelation of the origin of shape-selectivity in n-heptane hydroisomerization are useful for hydroisomerization catalyst design.