The invention provides a preparation method of an ecological fruit vinegar drink, comprising the following steps: 1, preparing microbial strain fermentation liquid containing lactobacillus, bifidobacterium, saccharomycete and Enterococcus faecium; 2, taking fresh fruit, washing, airing, draining and then squeezing into fruit juice; and 3, adding the fruit juice into a fermentation tank containing the microbial strain fermentation liquid, evenly mixing and stirring, sealing, covering tightly, and then fermenting at the temperature of 30-38 DEG C for 24-48h. The preparation method has the advantages that the ecological fruit vinegar drink product prepared by the method contains viable probiotic microecologics, integrates the functions of nutrition and health care, prevention and treatment of diseases, toxin excrement and beauty reservation, and is a green drink with obvious functions and effects. In addition, the preparation invention has wide raw material source, i.e. waste fruit such as broken fruit, fallen fruit, extruded and damaged fruit and the like can be taken as raw materials and then is fermented and purified by probiotics to obtain the favorite green drink of people, thus turning waste into wealth; and the preparation method has less energy consumption, small investment of production equipment, thus being a resource-saving and environmental-friendly development project.