Ottelia acuminata (Gagnep.) Dandy is a submerged plant that is sensitive to the eutrophication of its habitat. However, some researchers argue that O. acuminata has a purification effect on eutrophic waters. Until the 1960s, O. acuminata was the dominant species in Dianchi Lake, but it gradually disappeared beginning in the 1970s and is now extirpated. Recently, there has been progress regarding its restoration. However, there is controversy concerning the direct utilization of eutrophic lake sediment as the substrate for replanting O. acuminata versus the improvement of eutrophic lake sediment by adding soil with low nutrient content. According to analysis the parameters of chlorophyll a fluorescence induction kinetics,the net photosynthesis rate, the leaf number and leaf length of O. acuminata on the different substrates, the result shows that the photosynthetic capacity of O. acuminata planted in Dianchi Lake sediment and Er'hai Lake sediment was greater on day 40 than when planted in the other sediments. Further, the net rate of photosynthesis of O. acuminata planted in the red soil was 63.6% of that observed upon planting in the Er'hai Lake sediment, and the maximum fluorescence and variable fluorescence decreased 52.5% and 58.8%, respectively. The electron transport flux per reaction center of O. acuminata planted in the red soil was 59.7% that of when it was in Er'hai Lake sediment, the maximum photochemical efficiency of PSⅡ, density of reaction centers, and the performance index on absorption basis were lower than in the other samples. However, the dissipated energy flux per reaction center was 2.48 times that of the plants in the Er'Hai Lake sediment. These results indicate that O. acuminata planted in the red soil exhibited weaker performance and weaker photosynthetic capacity. By day 80, the photosynthetic indices of the samples had changed. The photosynthetic capacity of O. acuminata in the red soil increased substantially, and the net photosynthesis rate and absorption-based performance index also exhibited similar changes. There was no difference between plants in the red soil and those in the Er'hai Lake sediment. Although the photosynthetic capacity of O. acuminata in the red soil had recovered by day 80, leaf length was dramatically shorter than the plants in the other groups. At the same time, the photosynthetic capacity of O. acuminata planted in sand of Lake dramatically declined, while others increased, and the net photosynthesic rate was lower than in the other groups. The density of the reaction centers also declined observably. Combined with the physicochemical properties of the different substrates, the acidity of the red soil is potentially what led to the initial low photosynthetic capacity of O. acuminata. The acidic soil in an anaerobic environment would increase the soil pH in the later stage and hence facilitate the recovery of the photosynthetic capacity to a normal state. However, leaf length had not increased by day 80, which indicates that it was affected by the accumulation of photosynthetic product. The decline of the photosynthetic capacity of O. acuminata in sand of Lake is likely attributable to exhaustion of nutrients in the water. Therefore, we conclude that the direct utilization of eutrophic lake sediment as a substrate is an efficient method for the restoration of O. acuminata. Additionally, lake sediment nutrients will not limit the growth of O. acuminata, while the acidic red soil will.