The invention discloses a hydrogenation catalyst, a preparation method and an application method thereof. It uses organic phosphonic acid and molybdenum source as reaction raw materials, utilizes the reaction of the two, and bonds the two together to prepare a hydrogenation catalyst. Among them, the inventors found for the first time that P in the organic phosphonic acid can change the surface acidity of the active phase, increase the surface acidity of the hydrogenation catalyst after sulfidation, and the increase in acidity helps to enhance the hydrogenation activity of the hydrogenation catalyst; in addition, the presence of P has It helps stabilize asphaltenes, thereby inhibiting asphaltene condensation and coking, thereby reducing the amount of coke, slowing down catalyst deactivation, and finally reducing the coking rate and increasing the hydrogenation yield. At the same time, it is also found that the presence of P helps to change the structure of the active phase in the hydrogenation catalyst, which can reduce the amount of molybdenum with a tetrahedral structure that is difficult to vulcanize, and increase the amount of molybdenum with an octahedral structure that is easy to sulfide, which in turn facilitates the sulfuration of molybdenum. In the process, it is converted into molybdenum disulfide with suitable stacking layers, thereby increasing the activity of the hydrogenation catalyst and increasing the hydrogenation yield.