Qinghai Lake and Zhuye Lake, ∼400 km apart, are located in the northwest margin of the Asian summer monsoon. Water of these two lakes mostly comes from the middle and eastern parts of the Qilian Mountains. Previous studies show that the Holocene climate changes of the two lakes implied from lake records are different. Whether lake evaporation plays a role in asynchronous Holocene climate changes is important to understand the lake records. In this paper, we used modern observations beside Qinghai Lake and Zhuye Lake to test the impact factors for lake evaporation. Pan evaporation near the two lakes is mainly related to relative humidity, temperature, vapor pressure and sunshine duration. But temperature has different impacts to lake evaporation of the two lakes, which can affect Holocene millennial-scale lake level changes. In addition, differences in relative humidity on the millennial-scale would be more significant, which also can contribute to asynchronous lake records.