A method and system for producing hawthorn fermented beverage where hawthorn fruits are used as the main material to produce a hawthorn fermented beverage with special fermented flavor, rich nutrition, mellow mouth feel and suitable sourness and sweetness, through the processes of fruit sorting, cleaning, juice squeezing, blending, pre-sterilization, alcoholic fermentation, acetic fermentation, lactic acid fermentation, filtration, sterilization and filling. An atomized fermentation technology is adopted for the yeast aerobic proliferation during the alcoholic fermentation phase and for the acetic fermentation phase, so that, as compared with the liquid submerged fermentation methods, the fermentation time of these two stages are shortened by 10-15 hours and 62-100 hours respectively, and the fermentation period is shortened by 3-5 days, which improves the production efficiency of fermentation.