The invention provides a copper-based methanol synthesis catalyst and a preparation method thereof. The method includes the steps that copper-zinc mixed liquor is mixed with a first precipitator aqueous solution in a parallel flow mode, the pH is controlled to be 7-8, standing is performed for ageing, and slurry A is formed; a second precipitator aqueous solution is added into a soluble aluminum salt aqueous solution, the pH is controlled to be 7-8, the temperature is controlled to be 40-50 DEG C, standing is performed for ageing, and slurry B is obtained; the slurry A and the slurry B are mixed and filtered, a solid phase is washed, dried, roasted and formed, and the copper-based methanol synthesis catalyst is obtained. According to the preparation method, the steps are simple, the controllability is high, the raw material source is wide, and industrialization is easy to achieve; by the adoption of the preparation method, the copper-based methanol synthesis catalyst with high catalytic activity and heat stability can be obtained and is suitable for producing methanol with synthesis gas containing CO, CO2 and H2 under the low temperature and low pressure conditions; besides, the catalyst does not need reduction before use and can be conveniently applied and popularized on a large scale.