The invention discloses a seabuckthorn-snow daisy fruit vinegar beverage and a preparation method thereof. The preparation method comprises the following steps of: selecting, cleaning, crushing, performing heat treatment, enzyme treatment, juicing and filtering seabuckthorn fruits, respectively performing ultrasound-enhanced liquid deep alcohol and ultrasound-enhanced liquid deep acetic acid for batch fermentation on seabuckthorn pulp and snow daisy, filtering and blending, evenly mixing 1-40wt% of seabuckthorn-snow daisy acetic acid fermentation undiluted liquid, 5-10% of honey, 5-10% of sucrose, 10-30% of clear seabuckthorn juice and 10-70% of purified water, filtering, sterilizing and filling to obtain the seabuckthorn-snow daisy fruit vinegar beverage. According to the invention, key technologies such as composite enzymatic hydrolysis juicing technology, multifrequency ultrasound-enhanced efficient liquid batch fermentation technology and fermentation synchronous extraction technology are used to prepare the natural seabuckthorn-snow daisy fruit vinegar fermentation beverage which has wide practicability.