The submerged macrophyte communities have developed rapidly in the littoral zone of Lake Fuxian since 1960s, however, the monitoring frequency is relatively insufficient. To understand the distribution status and community changes of submerged macrophytes in Lake Fuxian during the past 60 years, we investigated and sampled the whole-lake submerged macrophytes and epiphytic filamentous algae from 41 sample sites in July 2016. The distribution of submerged macrophytes in the whole lake was determined by CBERS 04-based normalized difference vegetation index (NDVI) of August 18, 2016. In addition, the average biomass density, dominance index and the Shannon-Wiener diversity index in the coastal vegetation area were calculated. The results showed that the distribution area of submerged macrophytes in the summer of 2016 was 5.14 km². The average biomass (fresh weight) density was 9.8 kg/m², and the highest value was 48.7 kg/m². The total biomass (fresh weight) of the submerged macrophytes in the whole littoral zone was 5.02×10⁴ t. Totally 13 species of submerged macrophytes were collected, belonging to 5 families and 6 genera. Among the species, Ceratophyllum demersum had the highest biomass density, followed by Hydrilla verticillata and Myriophyllum spicatum. The species with the highest frequency of occurrence were M. spicatum, followed by Vallisneria natans and Potamogeton pectinatus. In addition, the species with the greatest dominance were M. spicatum, followed by C. demersum and H. verticillata. The Shannon-Wiener diversity index of submerged macrophytes in Lake Fuxian was between 0.05 and 1.28, having an average value of 0.75. Except for charophytes, the canopy of higher plant groups ranged from 1.5 m to 4 m, with the highest canopy of C. demersum. The biomass of epiphytic filamentous algae attached to the canopy of submerged macrophytes was much higher than that attached to the substrates, and filamentous algae mainly attached to the canopy of submerged plants within 100 cm along apical height. The historical data showed that the distribution area, total biomass and species richness of submerged macrophytes in Lake Fuxian increased sharply since 1957. The dominance of low meadow-forming species, such as charophytes and V. natans declined in recent years. In contrast, the tall canopy-forming submerged macrophytes such as M. spicatum and C. demersum dominated the community. The exotic species Elodea nuttallii emerged in recent years and became subdominant species. The epiphytic filamentous algae boosted, and most of them attached on the canopy of submerged macrophytes. At present, the submerged plant community in Lake Fuxian is at the highest stage of biomass, distribution area and diversity, which is the key period for protecting and maintaining the submerged macrophyte bed in the littoral zone. While, the dominance of tall canopy-forming species, the fast development of the exotic species and the bloom of the epiphytic filamentous algae may lead the submerged macrophytes community toward a structure composition which is common in eutrophic lakes. Therefore, it is urgent to control the nutrient loadings in Lake Fuxian and to harvest the upper crown within 100 cm of the tall species to control both the canopy-forming submerged macrophytes and the filamentous algae attached to them. These measures will create conditions for the development of the meadow-forming species and maintain the macrophytes community composition in oligotrophic lakes.