Currently, there is a shortage of lotus leaf pectin-type polysaccharide (LLP)-based prebiotic functional foods due to its low extraction efficiency and indistinct prebiotic and functional properties. In the study, medium-temperature alkali water, deep eutectic solvent, high pressure homogenization-assisted dual enzyme, and reflux extraction methods were used to screen out a process for LLP with high extraction efficiency, in vitro prebiotic activity, and functionality. It was demonstrated that LLPs prepared by high pressure homogenization-assisted dual enzyme, deep eutectic solvent (choline chloride and urea) and reflux extraction methods showed excellent prebiotic activities. Among them, LLP prepared by high pressure homogenization-assisted dual enzyme extraction (LLP-EP) had high extraction efficiency, high purity, high content of RG-I domain, fine homogeneity, low esterification degree, strong in vitro prebiotic activity, and comprehensive functional properties i.e. good water dispersibility and stability, rheological property, and emulsification stability. According to the structure-activity relationship analysis using a series of partially acid-hydrolyzed LLP-EP as prebiotics, the prebiotic activity of LLP-EP was mainly depended on high content of RG-I domain. These findings indicated that LLP had the potential to be used in beverages-based prebiotic functional foods, and also provided the theoretical basis for structural features of pectins to be better prebiotics.