The ecological evolution of lakes and their watersheds and the driving mechanisms are a key topic in paleoenvironmental research. However, the relative impacts of human activities and climate change on lake ecosystems since the last deglaciation remain unclear. We conducted a high-resolution study of the chain length distribution and concentration of n-alkanes in a sediment core from Lake Qilu in SW China, to reveal the ecological changes and their controlling factors since 14.6 cal kyr BP. Based on studies of modern samples, short-chain, medium-chain, and long-chain n-alkanes are associated with bacteria/algae, aquatic plants, and terrestrial plants, respectively. Combining the ACL17–33, Paq, and Σn-alkane indices, we found that both aquatic and terrestrial plants proliferated at Lake Qilu from 14.6 to 6 cal kyr BP, which was associated with a relatively warm and wet climate and dynamic strong winds. During the interval from 6 to 2 cal kyr BP, aquatic plants flourished, accompanied by a rapid surge in the regional productivity, primarily due to human activities. After 2 cal kyr BP, anthropogenic eutrophication was the primary cause of the increase in bacteria and algae populations. These results suggest that, before 6 cal kyr BP, climatic factors dominated the n-alkanes distribution; whereas after 6 cal kyr BP, human activities became the primary factor controlling the n-alkanes and ecological changes in Lake Qilu.