Red dragon fruit peel is a pectin-rich fruit waste that is a potential source of prebiotics and whose different sources and structures will influence its prebiotic function. Thus, we compared the effects of three extraction methods on the structure and prebiotic function of red dragon fruit pectin, the results showed that the citric acid extracted pectin produced a high Rhamnogalacturonan-I (RG-I) region (66.59 mol%) and more side-chains of Rhamnogalacturonan-I ((Ara + Gal)/Rha = 1.25), which can promote bacterial proliferation significantly. The side-chains of Rhamnogalacturonan-I may be an important factor in that pectin can promote the proliferation of B. animalis. Our results provide a theoretical basis for the prebiotic application of red dragon fruit peel.