The catalytic hydrodesulfurization (HDS) reactions of COS and CS2 with Mo3S9 cluster have been systematically investigated as a part of HDS of industrial feedstocks by DFT-based method. A detailed description of mechanisms is given, and different pathways are discussed and compared. It is found that the S in COS and CS2 will be hydrogenated, and the reactions will lead to formations of H2S, CO and CS. Comparing with COS, CS2 reacts with lower activation free energy and shows more reaction activity.