In this work, zeolite catalysts having different porosity in nano range were synthesized. For this, a zeolite-containing rock with a mordenite content of 72 wt% was treated with hydrochloric acid solutions of various concentrations. Impregnation of acid-modified samples with nickel in an amount of 1-2.5 wt% was aimed at obtaining different isomerization activity of the catalysts. The catalysts were characterized using XRD, low-temperature N-2 ad(de)sorption, TEM, and tested in micro pulse isomerization of linear hexane to estimate their selectivity in the formation of dimethyl-branched isomers. It has been shown that the low-concentrated acid increases the micropore volume by removing impurities from the zeolite micropores while the more concentrated acid also develops mesoporosity, especially the nanoscale pores phi similar to 2.3 nm. The upper limit of the Ni content (2 wt%) was found in the investigated catalysts providing the maximum efficiency of isomerization and formation of dimethylbutanes, and existence of the limit has been explained. It has been shown that upon isomerization of n-hexane on the acid-modified mordenite-containing rock, the formation of dimethylbutanes is not regulated by shape selectivity despite the larger kinetic diameter of the molecules as compared to mono-branched isomers. On the contrary, dimethylbutanes are more selectively formed inside zeolite micropores than in mesopores. The role of mesopores, mainly the regular system of nanoscale pores phi similar to 2.3 nm, is limited to providing transport routes for the reagents and reaction products.