In this study, we explored the use of magnetic-induced electric field (MIEF) treatment at various excitation voltages to assist three-phase partitioning (TPP) methods in extracting and separating pectic polysaccharides (PFPs) from the peel of fresh passion fruit (Passiflora edulis f. flavicarpa). The findings indicated that applying MIEF treatment prior to TPP separation significantly reduced the total sugar and galacturonic acid contents, as well as the degree of esterification of PFPs, with increasing excitation voltage. This treatment notably enhanced their yields and molecular weights. Although the MIEF treatment did not alter the monosaccharide composition of PFPs, it significantly modified their molar ratios of monosaccharides, thereby altering the backbone structure and neutral sugar side chains, which resulted in varied microstructures. Furthermore, especially at higher excitation voltages (≥300 V), the MIEF treatment improved the thermal stability, rheological, and emulsifying properties of PFPs. Consequently, our data suggest that the MIEF-assisted TPP method is a promising approach for the efficient and environmentally friendly preparation of pectic polysaccharides from plant materials.