Lake palaeoecology is an important branch of palaeolimnology, which aims to reconstruct the evolution of lake ecosystems on various spatiotemporal scales, and answer the questions of ecology, global change and environmental management through multiple subfossil biological proxies in the sedimentary records. This paper reviewed the history of palaeoecology studies at home and abroad. After introducing the fundamental principles of lake palaeoecology, this paper further elaborated the main progresses and achievements of palaeoecology research in China in the past 20 years, including (1) the transfer function models to quantitatively reconstruct past climate and environmental parameters (temperature, salinity, total phosphorus, etc.) based on a variety of biological and biomarker compound proxies were established; (2) the laws of the lake ecological environment evolution in different geological historical periods and in the past century, and its response characteristics and mechanisms to the natural and anthropogenic driving forces were revealed; (3) the palaeoecological records were used to diagnose the regime shift patterns and early signal characteristics of lake ecosystems, and the relationships between the biological structures and resilience loss of lake ecosystems were quantitatively revealed. These results provide important basis for lake environmental management and governance. In the end, the paper makes a prospect for the study of lake palaeoecology in China and puts forward the emphasis for the future studies.