As the Aral Sea shrinks, the lakebeds are gradually drying up, and the newborn Aralkum Desert (AD) has become one of the most active sands and dust storms (SDS) sources in Arid Central Asia (ACA). However, the temporal characterization of SDS activity and its possible driving factors have yet to be thoroughly investigated. Here, we studied the temporal variations of the SDS activities in the Aral Sea during 2000–2020 based on the Enhanced Dust Index (EDI), then investigated the relative importance of different drivers of SDS activities during the different phases. The findings revealed that the SDS activities increased during the past 20 years (2000−2020). The spring season is the most active period of SDS, especially in April. Additionally, the peak date of SDS activities has arrived earlier in recent years (2019–2020). Both climate and terrestrial factors strongly influence the temporal characteristics of SDS. The main driving factors of SDS actives vary in different phases. From 2000 through 2005, wind speed is the primary driving factor (r = 0.867, p <0.001). From 2006 to 2015, the SDS activities were dominated by soil characteristics and water area. Although SDS activity experienced a quiet period in 2016 due to lake recovery and changes in soil water content, the regional drought manifested by precipitation and relative humidity has played a vital role in the active SDS since 2016. The regional drought and continued falling water level will increase the SDS risk in 5–10 years. The Pre-Aral region—Amu Darya delta is the most vulnerable region to SDS because of its location downwind from the SDS source area. The study findings provide essential information for the prevention and mitigation of SDSs in the Aral Sea region. Given the growing uncertainty about the Aral Sea crisis, more attention should be paid to the SDS risk assessment, providing a scientific basis for regional sustainable development.