The residue of Citri Reticulatae Pericarpium (CRP) after the extraction of essential oils and flavonoids is a by-product in the CRP industry, and its utilization is often neglected. However, the residue (CRPR) contains many functional pectic polysaccharides. In the study, cellulase, alkali and deep eutectic solvent (DES)-water system were used to extract pectin (CRPP) from CRPR. Compared with the CRPPs extracted by cellulase, alkali and the other DES-water systems, CRPP extracted by DES-water system containing 80 % (v/v) choline chloride: urea = 1:2 (molar ratio) and 20 % (v/v) deionized water (DES-Ur) had high yield (21.31 %), proportion of rhamnogalacturonan-I domain (79.77 %) and degree of branching (9.21), which was due to the strong destructive effect of DES formed by choline chloride and urea on cell wall polysaccharides and the moderate modification of target polysaccharide by unique solvent environment. The good prebiotic activity i.e. proliferative ability on gut beneficial microbiota and slow fermentation rate of CRPP extracted by DES-Ur was proved by in vitro fermentation experiments. The study provided a theoretical and methodological basis for the green and efficient recovery of pectic polysaccharide from CRPR to realize the deep processing and utilization of CRP industry.