The invention relates to ferment jelly, in particular to nectarine and pomegranate collagen ferment jelly as well as a preparation method and application thereof. Mixing fruits and vegetables, adding cane sugar, pulping, pasteurizing, and cooling to room temperature to obtain fruit and vegetable pulp; adding cellulase and pectinase, and performing enzymolysis to obtain enzymatic hydrolysate; adding primary zymophyte, and fermenting to obtain primary fermentation liquor; adding secondary zymophyte composed of lactobacillus plantarum, lactobacillus acidophilus, lactobacillus paracasei and streptococcus thermophilus for fermentation, and filtering to remove impurities to obtain secondary fermentation liquor; the preparation method comprises the following steps: adding honey peach and pomegranate collagen enzyme into a stirrer, adding a protective agent which comprises trehalose, xylitol, amino acid, glycerol and hydroxypropyl-beta-cyclodextrin, adding collagen peptide and pre-dissolved agar, uniformly mixing, adding cheese powder, uniformly mixing, and cooling to obtain the honey peach and pomegranate collagen enzyme jelly. The nectarine and pomegranate collagen enzyme jelly prepared by the preparation method disclosed by the invention is high in SOD activity, relatively high in heat resistance and low temperature resistance, capable of preventing enzyme inactivation and long in shelf life.