The invention relates to a method for preparing pome south vinegar, comprising the following steps: the pome south is crushed and pulped as well as is subjected to color protection and enzymolysis, active dry yeast is taken as yeast wine to perform the alcohol fermentation, As.1.41 acetic acid bacteria are taken as parent bacterial strains, the composite mutagenesis consisting of ultraviolet mutagenesis and pulsed light mutagenesis is adopted to culture excellent acetic acid bacterial strain so as to perform the acetic acid fermentation, and the health care fruit vinegar is prepared by matching raw materials such as a sweetening agent, an acidity regulator, a flavoring agent and oligose. The process flow comprises the following steps of selecting pome south, cleaning the pome south, crushing and pulping the pome south, protecting the color, performing the enzymolysis, filtering and clearing, adjusting the component, performing the alcohol fermentation, performing the acetic acid fermentation, filtering, matching, evening materials, bulking, sterilizing and preparing the pome south vinegar. The technical proposal is feasible. The produced pome south vinegar has rich nutrient value, simple technique, low cost and easy industrialized production.