The invention discloses a pure alpha-phase molybdenum carbide-loaded noble metal catalyst, and a preparation method thereof. The preparation method comprises the following steps: (1) a noble metal salt solution is mixed with an ammonium paramolybdate water solution, and stirring is carried out; filtering and washing are carried out; and an obtained precipitate is dried, such that a precursor is obtained; (2) the precursor obtained in the step (1) is subjected to a non-equilibrium plasma treatment, such that noble metal-loading molybdenum oxide is obtained; and (3) the noble metal-loading molybdenum oxide obtained in the step (2) is carbonized with a carbon source gas under a temperature of 580-800 DEG C. According to the invention, a traditional roasting process is replaced by the non-equilibrium plasma treatment process. The pure alpha-phase molybdenum carbide-loaded noble metal catalyst can be directly obtained through a one-step carbonization process of the noble metal-loading molybdenum oxide obtained by the treatment process, such that a highly polluting nitridation process is eliminated. The invention also discloses an application of the prepared pure alpha-phase molybdenum carbide-loaded noble metal catalyst in a water gas shift reaction. As a result, the catalyst has excellent water gas shift performance.