An efficient ultra-high pressure (UP) compound enzyme extraction (UPEE) technology was used to extract and modify polysaccharides (U-RPPPs) from red Pitaya (Hylocereus polyrhizus) peels (RPPs), contributing to the increase yield and antioxidant activity as well as improvement of polysaccharides’ physicochemical and functional characteristics. Three polysaccharides (RPPP-1, RPPP-2 and RPPP-3) were isolated and purified from U-RPPPs by using a combination of ultra-filtration and gel permeation chromatography. Compared with heat reflux extraction polysaccharide (H-RPPPs), the extraction yield, uronic acid content (UAC), total phenols content (TPC), total flavonoids content (TFC), water solubility (WS), water holding capacity (WHC), oil holding capacity (OHC) of U-RPPPs were increased by 93.45%, 53.57%, 19.37%, 40.37%, 0.87%, 42.38%, 18.85% respectively, and molecular weight (MW), degree of esterification (DE) and protein content (PC) were decreased by 27.89%, 38.85% and 12.20% respectively, which significantly enhanced antioxidant activities including FRAP by 44.26%, DPPH· by 37.50%, ·OH by 26.59% and ·O₂⁻ by 27.27%, respectively. Among the three fractions, RPPP-1 had the lowest MW and DE, the highest contents of TPC, TFC, galacturonic acid (GalA), galactose (Gal) and rhamnose (Rha), exhibited good WS, WHC, favorable thermal stability, and showed the best antioxidant activities in a dose-dependent manner. These findings demonstrated that UPEE was an effective method to increase the extraction yields, improve the functional properties and bioactivities of pectic polysaccharides, which has enormous potential in the food industries.