In this study, Y zeolite nanocrystals were synthesized without an organic template and were used as a support for bifunctional nanocatalysts in the hydroisomerization of n‐octane. Different types of catalysts were synthesized by loading Pt, Cr, and phosphomolybdic acid (HPMo) on Y zeolite nanocrystal supports and were characterized by X‐ray diffraction (XRD), Brunauer–Emmett–Teller (BET), field emission scanning electron microscope (FE‐SEM), and transmission electron microscope (TEM) analysis. The Cr‐Pt/HPMo‐Y nanocatalyst with a surface area of approx. 600 m2/g showed the best performance in the hydroisomerization of n‐octane. The optimization of n‐octane hydroisomerization over bifunctional nanocatalysts supported on nanocrystalline Y zeolite, in the presence of H2 gas, was applied based on the response surface methodology (RSM) and Box–Behnken design (BBD) template. The effect of three different process variables on the yield of iso‐alkanes as the purpose process was determined. Experiments were carried out using a fixed‐bed microreactor under different ranges of weight hourly space velocity (WHSV) (A = 0.5–1.5 hr−1), H2 to n‐C8 molar ratio (B = 1:1–3:1), and reaction temperature (C = 200–300°C). The RSM proved that the temperature variable had the greatest impact on the hydroisomerization reaction yield.