We studied on the function of Pd species located in mesopores and inside zeolite channels (micropores) of the montmorillonite-modified zeolite catalyst for the hydrodesulfurization of diesel fraction with 350 ppm of sulfur as DBT, 4-MDBT, and 4,6-DMDBT. It was shown that the ex-dihydrogentetrachloropalladate impregnated catalyst as well as the ex-tetraamminepalladium(II) chloride ion-exchanged catalyst have high efficiency of sulfur removal from the diesel fuel in temperature range 280–300 оC. The sulfur tolerance of catalyst depended on the method of Pd adding. The catalyst prepared by ion-exchange with tetraamminepalladium chloride solution exhibited the highest sulfur tolerance. According to FTIR of adsorbed CO, this catalyst contains a small Pd metal atoms or cluster in electron-deficient state inside zeolite channels. They probably ensure sulfur tolerance due to hydrogen spillover. The montmorillonite addivite significantly modifies performance of the Pd-Zeolite catalyst in hydrotreating of diesel fraction. It leads to a decrease of cracking function, while those of hydrogenolysis of sulfurorganic molecules and hydrogenation of aromatic molecules are strengthened in comparison with the unmodified catalyst. This effect is explained by the change of acidic properties of the catalyst, limitations of diffusion of various molecules into the zeolite channels, and diffusion of Pd from the zeolite channels.