Studying the distribution of submerged macrophytes and the influencing factors of water environment is of significance for the recovery of submerged macrophytes in Lake Dianchi. Field surveys for characteristics of submerged macrophytes were carried out at 24 typical regions in Lake Dianchi from April to November, 2016. A total of 9 submerged macrophytes species were recorded in the 16 study regions. Potamogeton pectinatus, P. maackianus, Myriophyllum spicatum, Hydrilla verticillata and P. wrightii were the main submerged macrophytes species in Lake Dianchi. The depth of submerged macrophytes was less than 3 m, which was 10% of the whole lake area. Principal component analysis showed that total nitrogen, total phosphorus, suspended solids, chemical oxygen demand, transparency and chlorophyll-a were the main influencing factors for the distribution and biomass of submerged macrophytes, whereas transparency was the main influencing factor for the coverage of submerged macrophytes. Canonical correspondence analysis indicated that the distribution of submerged macrophytes was mainly influenced by nutrient concentrations and chemical oxygen demand. M. spicatum and H. verticillata are tolerant species of organic matter concentration, and algae. P. wrightii and S. pectinata are adaptive to high nutrients concentration. Reducing chemical oxygen demand and algae biomass will be crucial to submerged macrophytes restoration, with controlling the nutrients level in water as the second. According to the principle of "one district one policy", the inside of Dongfeng dam and the southern lake should be the prior place to be restored, while the northern lake should be the place to control algae at first. The eastern lake should cut down the organic matter and nutrients concentrations. The western lake should be under natural protection.