Low methoxyl pectin (LMP) with different degree of methoxylation (DM, 40–50 %, 20–30 % and 5–10 %) were prepared from commercially available citrus pectin using high hydrostatic pressure assisted enzymatic (HHP-pectin) and traditional alkaline (A-pectin) de-esterification method. The results showed that both de-esterification methods and DM exhibited LMPs with varied physicochemical, structural, and functional properties. As the DM decreased, LMP showed a decrease in molecular weight (Mw), while an increase in negative charges and rhamnogalacturonan I (RG-I) ratio, accompanied with better emulsion stability, emulsion gel strength and water-holding properties. Relative to A-pectin, HHP-pectin had higher Mw and lower RG-I side chain ratio, contributing to its better thermal stability, apparent viscosity, and emulgelling properties. HHP-pectin with lower DM (5–10 %) showed superior thickening, emulsifying and emulgelling properties, while that with higher DM (40–45 %) had superior thermal stability, which provided alternative for de-esterification and targeted structural modification of pectin.