Regime shifts in shallow lakes can lead to great changes in ecosystem structures and functions, making ecosystem management more complicated. Lake Yilong, located in Yunnan Province, is one of the most eutrophic lakes in China. Although there is a high possibility that this lake has undergone regime shift one or more times, the presence of regime shifts and their drivers remain unknown. Here, we employed the sequential t-test analysis of regime shifts to detect the regime shifts based on the long-term (1989–2018) dataset of the lake. We further determined their potential drivers, and explored the nutrient thresholds of regime shifts and hysteresis. The results showed that during the testing period, three regime shifts occurred in 1996 (restorative type), 2009 (catastrophic type) and 2014 (restorative type). The potential key drivers for the first two regime shifts (1996 and 2009) were both related to aquaculture. The abolition of cage fish culture may have led to the restorative regime shift in 1996, and the stocking of crabs and excessive premature releasing of fry possibly caused the catastrophic regime shift in 2009. However, the third regime shift, which occurred in 2014, was possibly related to the drought and succedent hydration. These results indicate that adjustments of aquaculture strategy and hydrological conditions are critical for the lake ecosystem’s recovery. Moreover, the total phosphorus thresholds were identified to be lower than 0.046 mg/L (restorative type) and higher than 0.105 mg/L (catastrophic type), respectively. In addition, an obvious hysteresis was observed after 2014, suggesting that nutrient reduction is important for this lake’s management in the future.