Abstract: In restoration of aquatic vegetation in the degraded area of shallow lakes, it is necessary to study the effects of low light stress and sediment types on aquatic plants. Vallisneria natans has strong tolerance to low light and sediment, and can be selected as a restoration species. The central part of the southern Erhai Lake (a mesotrophic lake in Yunnan Province, China) is flat, with an average annual water depth of about 6.3 m, which was called the “lake center platform” (LCP). Large areas of aquatic vegetation, including V. natans, was used to exist in LCP, it played important roles in the lake ecological function, but has completely disappeared since 2003. So, we chose V. natans as experimental material, and set two kinds of sediment conditions to study the morphological and physiological responses of V. natans under weak light of LCP and two kinds of sediment (clay and silt) environment, in order to explore the effect of substrate improvement on the restoration of V. natans. The results showed that: (1) Under the extremely low light environment, the survival number of V. natans decreased, and it also showed morphological and physiological responses to stress. The biomass and length of leaf and rhizome decreased in both sediments, and the contents of carbon (C), soluble carbohydrate and starch decreased, but the contents of free amino acid (FAA) and nitrogen (N) increased. The low light intensity inhibited the growth of V. natans and caused some plant deaths. (2) The effect of weak light stress on leaves in both sediments was greater than that on rhizome, which was shown in the increasing biomass ratio of rhizome and leaf. The physiological stress response of leaves was relatively greater than that of rhizomes, which was reflected in the decrease in the ratio of N and FAA contents, and the increase in the ratio of soluble carbohydrate and starch contents. (3) There were significant differences in the responses of V. natans to weak light environment under different sediment conditions, which was shown below: the survival number, starch content and biomass of rhizome in clay group were higher than those in sludge group, while FAA and N contents of leaves were lower. This attempt indicated that under the current water quality environment, it was possible to achieve the restoration of submerged plants in the LCP by combining with local sediment improvement.