In this study, the effects of modified maifanite loaded with magnesium ions as a substrate on the growth of submerged macrophyte Vallisneria natans (Lour.) Hara and its rhizosphere microenvironment were investigated to determine its suitability for application in the field of ecological restoration. Different doses of unmodified maifanite and modified maifanite (MM1, 200 g m-2; MM2, 400 g m-2; and MM3, 800 g m-2) were added to the sediment, and the growth and physiological indicators of V. natans were measured once a month. The changes in the rhizosphere microenvironment were also studied. The results revealed that, compared with unmodified maifanite, modified maifanite was more beneficial for increasing the plant height, and the most significant growth promotion effect was observed in the MM2 group at 150%. The MM2 group also exhibited the highest relative abundance of microorganisms, with Chao, ACE, and Sobs indices of 5799.64, 6087.99, and 4660, respectively. The addition of the substrate increased the abundance ratios of Desulfobacterota and Nitrospirota, indicating a possible improvement in the microenvironment quality at the bottom of eutrophic lakes. Compared with unmodified maifanite, modified maifanite enhanced the microenvironment quality at the bottom and the growth of submerged macrophytes to a greater extent, with the most pronounced effect observed at 400 g m-2. These findings demonstrate that modified maifanite can be effectively used as a substrate for improving ecological restoration projects for lakes.