Abstract: Citrus waste can be reused to promote the value-added of the citrus industry in recent years. Among them, free pectin can be developed to reduce the direct discharge of existing citrus waste for better ecological environments. This study aims to understand the differences in physical and chemical properties, structure, and function of different citrus pectins. The targeted application of pectin was also expanded to improve the added value of citrus by-products. Acid extraction was applied to extract the pectin from the peels of Shangrao pomelo, Gannan navel orange, Nanfeng honey tangerine, Japanese pomelo, small green citrus, and lemon, which were named HMP-1, HMP-2, HMP-3, HMP-4, HMP-5and HMP-6, respectively. A systematic analysis was made to explore the physical and chemical properties, structure, and gel properties of all six HMPs. There was basically a similar with the content of protein, ash, and various monosaccharides in the six HMPs. The results showed that all six HMPs were anionic polysaccharide and high ester pectin, where the esterification degrees ranged from 67.20% to 75.45%. There was a degraded degree during the extraction from the citrus processing by-products, in terms of the physicochemical properties and molecular structures. The molecular weight, viscosity, and molecular chain structure dominated the gel properties of pectins. The HMP-4 shared the largest molecular weight. All six HMPs formed the acid/sugar gels with high strength and intercepted water in a three-dimensional gel network. The better stability still remained after freezing and thawing cycles. The water holding capacity was above 96% in all six HMPs. HMP-1 and HMP-6 with the lower molecular weight shared the highest gel strength above 200°SAG. This was related to the high HG content and the complete molecular structure of HMP-1, as well as the higher RG-I content and branching degree of HMP-6. The weak gel strength of HMP-5 with the high molecular weight and viscosity was related to its molecular chain degradation and low RG-I content. While the HG contents of HMP-2, HMP-3, and HMP-4 were lower than those of HMP-1and HMP-6 and higher than that of HMP-5, where the gel strength was the same. The AFM images showed that the outstanding molecular chain cross-linking appeared in the HMP-1 and HMP-6. Shangrao pomelo and lemon peels were superior raw materials to extract the high methoxyl pectin. The peel pectin of Shangrao pomelo, Gannan navel orange, and lemon were suitable for the stronger gel systems, such as soft candy and jelly, while the peel pectin of Nanfeng honey tangerine, Japanese pomelo, and small green citrus were more suitable for the weaker gel systems (such as jam and yogurt), particularly for the foods that require both pectin and citrus fiber. In addition, the extremely high molecular weight of Japanese pomelo peel pectin was used as a dispersion stabilizer in protein milk beverages, in order to verify the dispersion stability and emulsifying performance. The physical and chemical properties, structure, and functional properties of different citrus pectins can provide a theoretical reference to determine the extraction materials with better gel properties, thus expanding the production and targeted application of pectins.