Increased human activity has caused a regime shift in lake ecosystem, which causes environmental and ecological problems such as biodiversity decline, algae blooms and deterioration of water quality. Many Chinese lakes have undergone regime shift or are facing the risk of abrupt change. It is essential to know the temporal and spatial differences of regime shift for the protecting lake ecosystem, preventing regime shift and formulating appropriate restoration strategies. This study collected paleolimnology data of 55 lakes in different regions of China and discussed the regional characteristics of lake mutations. The study determined the temporal and spatial differences of regime shift in lake ecosystem and revealed the reasons for the spatial differences. Our study found that the regime shift time of Chinese lakes has the characteristics of regional differentiation: regime shift time of lakes in the middle and lower reaches of the Yangtze River is much earlier than that of the whole country. Regime shift happens earlier in the east and northeast lake areas than in the southwest, Inner Mongolia and Xinjiang lakes. In various lake region, regime shift happens earlier in the suburban lakes than in rural lakes. The intensity of human activities is the main driving force for the temporal and spatial differences of regime shift. Lakes with slower warming but stronger human activities are more likely to undergo regime shift. Our result suggests that the intensity of regional human activities has affected the evolution progress of lake ecosystems and caused regional differences of the regime shift in Chinese lakes. From the perspective of abrupt change in ecosystem, this study uses paleolimnology data to summarize the evolution of Chinese lake ecosystems under human activities, achieves a deeper understanding of the current situation of Chinese lakes, and provides a strong scientific basis for lake protection.