As an emerging research topics of limnology, variations in water level play a key role in regulating water quality, volume and ecosystem function of lakes. However, the characteristics of plateau lake group located in central Yunnan of China have not been well studied. Taking Lake Dianchi, Fuxian and Yangzong as the study cases, the trends of water level were analysed based on Mann-Kendall statistic approach, and an index system related to fluctuations of water level were established with extreme precipitation index generated from RClimDex and other metrological index. Coupling multiple linear regression and principal factor model, a model for water level alteration of plateau lakes was built to distinguish main driving factors and their effects. Results showed that no significant trend was observed in the annual water level fluctuation of these lakes from 1988 to 2015. However, water level had a significant increase trend in Lake Dianchi at a rate of 0.025 m per year, while no trends found in the other two lakes. The extreme climate index in the lake basins had no significantly statistic trend of temporal alteration. Reverse trends of evaporations were observed in Lake Dianchi and Fuxian that have been decreasing by 21.05 mm per year and increasing by 5.52 mm per year, respectively. The trend of evaporation in Lake Yangzong was not pronounced. Variation of water level in Lake Dianchi can be explained by climatic indexes which accounted for 49.7% of total variation, indicating that water level change can be ascribed to the combined effects of anthropogenic activities and climatic conditions. By contrast, water level variations of Lake Fuxian and Yangzong were mainly influenced by climatic conditions. For Lake Yangzong, evaporation, amount of precipitation and days of consecutive precipitation accounted for 93.3% of variation of water level. Index of precipitation and dry spell can explain 64.5% of variation of water level in Lake Fuxian. Extreme precipitation indices play an important role in explaining water level change in plateau lakes.