The objective of this study was to extract and characterize pectins from diverse waste fractions of Citrus unshiu, which were aggregated with soy protein isolate and utilized to stabilize the oil droplets as high-internal-phase Pickering particles. All pectins extracted from flavedo, albedo, and pomace (extraction yield: 14.22, 17.56, and 14.33%, respectively) were found to be low-methoxyl with degrees of esterification of 27.40, 28.79, and 36.28%, respectively. Furthermore, all pectins exhibited shear-thinning behavior, with consistency index values of 5.13, 0.79, and 0.47 Pa·s for flavedo, albedo, and pomace, respectively. The average molecular weights were determined as 72, 29, and 7.4 kDa, respectively, based on the observed viscous behaviors. It is noteworthy that flavedo-extracted pectin demonstrated the highest dislocation density and glass-transition temperature among all the anmorphous pectins, a phenomenon that may be ascribed to its elevated calcium ion content (9.63 mg/g) and ionic interactions. The pectins were aggregated with soy protein isolate (SPI) at pH 3.5 and 4.0 through ionic and hydrogen interactions, and utilized to prepare high-internal-phase Pickering emulsions (HIPPEs). The HIPPEs that were stabilized with these aggregates demonstrated superior centrifugal and storage stabilities, with no phase separation, in comparison to those stabilized solely with either SPI or pectin. Consequently, the results suggest that pectins originating from Citrus unshiu waste have the potential to be used as a food additive, such as a stabilizer or emulsifier.