Poyang Lake is the largest freshwater lake in China. The relationship between the water level and the area of the Poyang Lake is of great significance in studying the changes of the ecological environment in the Poyang Lake. At present, the research on the relationship between Poyang Lake water level and area is different, and there are some uncertainties with ignoring the influence of water fluctuating on the water level and area of the Poyang Lake. Based on the consideration of water fluctuating, this paper analyzed the spatial distribution and causes of different areas of lakes under the condition of multiple surface areas of the same water level in the Poyang Lake, and studied the uncertainty of the relationship between the surface area and water level by using the measured level data of the Poyang Lake during 2000-2014 and the corresponding remote sensing image data. The results show that: (1) The relationship between the surface area and water level in the Poyang Lake is uncertain, which is mainly affected by the different water surface slope in the water fluctuating process in the Poyang Lake; (2) Under the same water level, the surface area of the Poyang Lake in the water rising process is often larger than that in the water falling process, and the changes on the variation of water surface area are consistent with those of the water fluctuating range; (3) The effects of water rising and water falling processes on the water level and area of the Poyang Lake are mainly at the low and middle water level. The water level rises with less impacts.