The rhamnogalacturonan I (RG-I) region of pectin shows health benefits and novel gel applications. Commercial pectin is extracted from citrus peel in most instances, whereas they are homogalacturonan (HG)-dominated productions and the methods to extract pectin targeting RG-I are limited. To take full advantage of citrus wastes and upgrading this pectin resources, a new extraction method based on a diluted NaOH assisted by a combination of ultrasound (US) and pressure, namely manosonication (MS), was established for RG-I enriched pectin extraction. MS significantly enhanced the pectin yield (21.47 ± 0.11%) while reducing the use of NaOH reagents (50 mmol/L) and processing time (50 min). Structurally, the MS (300 kPa) resulting products achieved nearly a 2-fold greater RG-I content (58.61 mol%) than that of commercial pectin (30.12 mol%). Moreover, for the investigation of the extraction mechanism, external pressure enhanced the cavitation effect, as the calorimetric intensity increased from 1.28 W/mL (100 kPa) to 3.3 W/mL (350 kPa). A sufficient ultrasonic mechanical action allowed for obtaining RG-I enriched products with large molecular weight (9.506 × 104–2.813 × 105) and low degree of methoxylation. Transmission electron microscopy (TEM) and scanning electron microscopies (SEM) verified the increased disintegration of the cell wall tissue by MS. Raman imaging and immunofluorescence labeling suggested the synergistic effect of pressure and ultrasound on enhancing the yields and RG-I content. This new method provided alternations in functional polysaccharides extraction, and the yield and structure of citrus RG-I enriched pectin strongly indicates the potentials of MS in other RG-I rich vegetables applications.