Development of highly efficient and long stable hydrodesulfurization (HDS) catalysts still is a great challenge for the refining industry. In this work, a series of intermetallic noble metal silicides supported by carbon nanotubes catalysts (Pt2Si/CNTs, RhxSi/CNTs, and RuSi/CNTs) have been developed by chemical vapor deposition successfully, using dichlorodimethylsilane as Si source. These materials were used as efficient catalysts for the deep HDS of dibenzothiophenes (4,6-DMDBT and DBT) and performed high selectivity to the direct desulfurization pathway. The sequence of HDS activity over noble metal silicides catalysts is in keeping with the sequence of HDS activity of the corresponding metal catalysts, which is Pt2Si/CNTs > RhxSi/CNTs >> RuSi/CNTs. In addition, the Pt2Si/CNTs performed an excellent stability in 100 h stability testing for HDS of 4,6-DMDBT. Therefore, this sulfur-tolerant noble metal silicides could be as promising catalysts for the ultra-deep HDS of fossil-fuel.