The invention discloses a hydrogenation catalyst which contains a carrier, an active component and an auxiliary. The active component and the auxiliary are loaded on the carrier, wherein the active component is ruthenium (Ru), the auxiliary is manganese (Mn) or a combination of Mn and at least one of metal components of an IB group, an IIB group, an IIIB group and a VIII group, and the carrier is a composite carrier of ZrO2 and ZnO. The invention further provides a preparation method of the hydrogenation catalyst and an application of the hydrogenation catalyst to 2-methyltetrahydrofuran synthesis. The hydrogenation catalyst has higher catalytic activity and 2-methyltetrahydrofuran selectivity and longer service life in the reaction that raw materials containing 2-methyl furan synthesize the 2-methyltetrahydrofuran through hydrogenation, and the raw materials containing the 2-methyl furan are not required to be rectified so that process is simplified, and energy consumption is reduced.