Constructing favorable morphology is considered to be an effective strategy to enhance the amphiphilic performance of materials. The directional alignment of ultra‐thin lamellar materials significantly facilitates utilization of active sites at the bi‐phase interface. Herein, an ultra‐thin amphiphilic C/Si shell pieces Janus material (d = 10.4 nm) prepared by graphene oxide and SiO2 is reported. The outer SiO2 layer is associated with hydrophilicity, while the inner C layer exhibits hydrophobicity. A Pickering emulsion interface catalyst for fuel oil oxidative desulfurization is constructed by impregnating an amino‐modified C/Si Janus material with keggin‐type HPW. The results demonstrate that amphiphilic catalyst with an ultra‐thin C/Si shell pieces exhibits superior performance in terms of emulsification rate (100%) and desulfurization rate (99.62%) in the O/W emulsion formed by n‐octane/acetonitrile. The catalyst demonstrates the advantages of easy recovery and regeneration, maintains a higher activity after oxidative desulfurization (ODS) process, and has higher industrial application value.