Low methoxyl pectin has received wide spread attention as a potential raw material for low-sugar foods, but its complex structural composition limits its application in the food field. To investigate the effect of structural differences of pectin on the properties of pectin-deacetylated konjac glucomannan (DKGM) composite gels, four low methoxyl pectins, namely citrus pectin, Ficus pumila Linn. seed pectin, Premna microphylla Turcz pectin and sunflower disk pectin were selected as raw materials to be composited with DKGM obtained directly from the preparation, and rheological, differential scanning calorimetry, and infrared spectroscopy were used to investigate the effects of pectin structure on the rheological properties and thermal stability of pectin-DKGM composite gels. The results showed that the addition of DKGM could improve the performance of pectin gel compared with single pectin gel, and the three natural low methoxyl pectins were more advantageous than the industrially prepared citrus pectins in the gel products. The composite gel hardness of Ficus pumila Linn. seed pectin with DKGM was the greatest, and the gel hardness was positively correlated with the homogalacturonan content of the pectin. Premna microphylla Turcz pectin formed the most hydrogen bonds with DKGM, which resulted in the best thermal stability and a denser gel structure. In addition, the molecular weight of the pectin had a greater effect on the gel properties of the composite gel than the degree of esterification and structural domain composition. The results could provide a better understanding of the effects of low methoxyl pectins with different structure on the properties of composite gels, and provide a theoretical basis for the development and application of pectin and DKGM in gel foods, as well as for the modulation of the quality of gel products through the structural properties of pectin.