Continuous climate warming in the last few decades has led to global climate anomalies, resulting in frequent drought events in arid/semiarid regions with fragile and sensitive ecological environment. The Mongolian Plateau (MP) is located at the mid-latitude arid/semiarid climate region, which is deemed as the most sensitive region in response to global climate change. In order to understand the spatiotemporal characteristics of droughts in Mongolian Plateau under changing climate, we divided the study area into three climatic regions via Köppen climate classification. Then, the seasonal and annual drought trends were analyzed by standardized precipitation evaporation index (SPEI), which is a function of monthly mean temperatures, highest temperatures, lowest temperatures and precipitations, collected from the 184 meteorological stations from 1980 to 2015. Mann–Kendall (MK) test was employed to detect if there is an abrupt change of annual drought, while the empirical orthogonal function method (EOF) was adopted to investigate the spatiotemporal characteristics of droughts across the Mongolian Plateau. Results from MK test illustrated that the SPEI-12 exhibited statistically significant downward trends (a < 0.05) for all three climatic regions of the Mongolian Plateau. EOF spatial analysis indicated that Region III experienced the most severe drought from 1980 to 2015. During the 35 years period, an abrupt change of drought was detected in 1999. Before year 1999, the climate was relatively humid. However, the entire region became more arid after year 1999, reflected by remarkably increased frequency and intensity of drought. SPEI-3 revealed the trend of drought at seasonal scale. We found that drought became more severe in spring, summer, and fall seasons for the entire MP. However, winter became more humid. Different climate regions exhibited quite different drought seasonality: Region I experienced a severe arid trend in summer and fall. For Region II and III, summer became more arid. All three regions became more humid in winter season, especially for Region I, with the Sen’s slope of 0.0241/a.