The invention discloses a preparation method of an apple pectin heteropolysaccharide for improving diversity of intestinal florae. The preparation method comprises the following steps: I, dissolving apple powder into water, performing enzymolysis, performing vacuum concentration, and performing purification so as to obtain a pectin extract; II, adding pectin methylesterase and pectin acetylase into the pectin extract, performing primary oriented digestion, adding polygalacturonase and pectate lyase, performing secondary oriented digestion, further adding polyrhamnogalacturonases, xylogalact uronase, galactan esterases and arabanase, and performing third oriented digestion so as to obtain a modified pectin extract; and III, performing purification treatment on the modified pectin extract, so as to obtain the apple pectin heteropolysaccharide. Through three times of oriented digestion, the apple pectin heteropolysaccharide which is high in neutral polysaccharide ratio, low in methyl esterification degree and low in acetylation degree can be obtained, the apple pectin heteropolysaccharide is capable effectively improving diversity of intestinal florae, and the microorganism fermentation degradation rate in intestines within 24 hours is greater than 80%.