Because of its nature, lake evaporation (E L ) is rarely measured directly. The most common method used is to apply a pan coefficient (K p ) to the measured pan evaporation (E p ). To reconstruct the long sequence dataset of E p , this study firstly determined the conversion coefficients of E p of two pans (φ20 and E601, each applied to a different range of years) measured synchronously at the nearest meteorological station during the unfrozen period through 1986 to 2001, and then E p was estimated by the PenPan model that developed to the Class A pan and applied to quantify the E L of the Juyan Lake, located in the hyper-arid area of northwest China. There was a significantly linear relationship between the E601 and φ20 with the conversion coefficients of 0.60 and 0.61 at daily and monthly time scales, respectively. The annual E p based on monthly conversion coefficients was estimated at 2240.5 mm and decreased by 6.5 mm per year, which was consistent with the declining wind speed (U) during the 60 years from 1957 to 2016. The E p simulated by the PenPan model with the modified net radiation (R n ) had better performance (compared to E p measured by E601) than the original PenPan model, which may be attributed to the overestimated R n under the surface of E601 that was embedded in the soil rather than above the ground similar to the Class A and φ20. The measured monthly E L and E p has a significantly linear relationship during the unfrozen period in 2014 and 2015, but the ratio of E p to E L , i.e., K p varied within the year, with an average of 0.79, and was logarithmically associated with U. The yearly mean E L with full lake area from 2005 to 2015 was 1638.5 mm and 1385.6 mm, calculated by the water budget and the PenPan model with the modified R n , respectively; the latter was comparable to the surface runoff with an average of 1462.9 mm. In conclusion, the PenPan model with the modified R n has good performance in simulating E p of the E601, and by applying varied K p to the model we can improve the estimates of lake evaporation.