The invention discloses a copper based catalyst used for hydrogenating carbon dioxide to synthesize methanol, and a preparation method and an application thereof. The preparation method of the catalyst comprises the following steps: 1, processing a zinc salt, an aluminum salt, a zirconium salt and a stabilizer to prepare a first solution, or processing the zinc salt, the aluminum salt and the zirconium salt to prepare a second solution; 2, processing carbonate and hydroxide to prepare a third solution; 3, processing a copper salt to prepare a fourth solution; 4, processing the first solution and the third solution to form a first precipitation solution, or processing the second solution and the third solution to form a second precipitation solution; 5, adding the fourth solution to the first precipitation solution to form a third precipitation solution or adding the fourth solution to the second precipitation solution to form a fourth precipitation solution, ageing after Cu in the precipitation solution precipitates, and washing; and 6, drying, and calcining. The catalyst contains 30-50% of Cu, 20-40% of Zn, 10-20% of Al, and 5-20% of Zr. The catalyst is used for a reaction for hydrogenating carbon dioxide to synthesize methanol.