Based on meteorological data collected over nearly 60 years (1960–2017) from four national meteorological stations along the margins of the Badain Jaran Desert, this study analyzed the spatiotemporal variations in evaporation from water surfaces and identified the dominant controlling factors. Methods used included linear trend analysis, linear tendency estimation, the departure method, the rank correlation coefficient-based method, and Multiple Linear Regression (MLR). Results indicate notable spatiotemporal differences in evaporation distribution and evolution. Spatially, average annual evaporation exhibited a pronounced altitude effect, decreasing at a rate of about 8.23 mm/m from east to west with increasing altitude. Temporally, annual evaporation showed significant upward trends after 1996 at the northeastern (Guaizi Lake) and western (Dingxin) margins, with rates of 132 mm/10a and 105 mm/10a, respectively. Conversely, along the northwestern (Ejina Banner) and southern (Alxa Right Banner) margins of the desert, an evaporation paradox was observed, with annual evaporation trending downward at rates of 162 mm/10a and 187 mm/10a, respectively, especially after 1987. The dominant factors controlling evaporation varied spatially: Average annual temperature and relative humidity influended the western margin (Dingxin), average annual temperature was the key factor for the northeastern margin (Guaizi Lake), and average wind speed was crucial for the northern (Ejina Banner) and southern (Alxa Right Banner) margins.