As a critical component of freshwater ecosystems, aquatic plants play an essential role in maintaining ecosystem structure, function, and stability. However, under global change scenarios, aquatic plants are facing multiple stressors such as eutrophication, climate warming, emerging pollutants, and biological invasions, leading to a significant decline in aquatic vegetation, particularly submerged macrophytes. Based on systematic research findings over the years from the Liangzi Lake National Field Station for Scientific Observation and Research, Wuhan University, this paper provides a comprehensive review of the major advances in the ecology of aquatic plants and ecosystem functions across individual, population, community, and ecosystem scales. At the individual and population levels, the environmental regulation mechanisms of ecological stoichiometry in aquatic plants were revealed, and the adaptive strategies of clonal integration and functional traits to heterogeneous habitats were elucidated. At the community level, the key regulatory factors of biodiversity-productivity relationships and mechanisms of interspecific interactions were analyzed. In invasion ecology, the mechanisms driving the invasion of exotic aquatic plants under environmental change and biotic interactions were systematically clarified, and the ecological effects of exotic plants on material cycling, epiphytic communities, and pollutant responses were evaluated. In terms of genetic evolution, multi-omics approaches were comprehensively employed to uncover the phylogeographic patterns, local adaptation mechanisms, and invasion potential of aquatic plants. In ecological restoration, long-term in-situ monitoring and restoration practices have verified the effectiveness of submerged vegetation reconstruction in controlling internal nitrogen and phosphorus loading, and new ideas for combined remediation technologies and biological regulation were proposed. These studies not only deepen the theoretical understanding of the relationship between ecological adaptation of aquatic plants and ecosystem functions but also provide important theoretical basis and practical guidance for the conservation, restoration, and sustainable management of freshwater ecosystems.