The distance between the two active sites of a bifunctional catalyst (acid sites and metal sites) is critical for the hydroisomerization performance. However, the influences of the dehydrogenation/hydrogenation species (Pt or Ni) and the intimacy between the acid sites and the metal sites over the distribution of the isomers have rarely been investigated. Herein, the bifunctional catalysts were prepared by loading the hydrogenation component (Pt or Ni) on γ‐Al2O3 or HZSM‐48 zeolite separately and then mixing them with equal mass of HZSM‐48 molecular sieves and γ‐Al2O3, respectively. The hydroisomerization performance of n‐dodecane was investigated on a fixed‐bed reactor. The loading position of the metal can directly affect the activity of the hydroisomerization reaction. However, the distribution of the isomer products is not affected by the loading position and the metal type (Pt or Ni) obviously, and the middle‐positioned isomer is the main isomer product regardless of the position and the type of the metal. The catalysis results indicate that the isomerization of n‐dodecane mainly follows the “Key‐Lock” catalysis mode on HZSM‐48.