The invention provides a preparation method of fruit ferment. The preparation method comprises the following steps: carrying out anaerobic fermentation by inoculating anaerobic bacterium strains, filtering the obtained fermentation products, saving the filtrate (A), keeping on inoculating aerobic bacterium strains to peels and dregs of fruits to carry out aerobic fermentation for 5 to 15 days, then adding liquor, keeping on fermentation for 5 to 10 days, then filtering the fermentation products, condensing the filtrates, then merging the condensed filtrates, adding molasses, inoculating beneficial bacteria to the mixed filtrate, and sealing the mixed filtrate for 10 to 20 days to obtain the environment-friendly ferment. The preparation method can effectively avoid the mildew of fruit peels during the fermentation process, thus the content of nitrite is reduced, the obtained ferment prepared from fruit peels is healthy and unique, at the same time, the ferment content is increased, the function of the ferment is improved, moreover, the wastes (fruit peels) are converted into valuable resources, and the utilization of wastes is promoted.