Algal bloom, which is caused by lake eutrophication, is one of the most serious environmental and ecological problems in the world. Lake Dianchi, the largest plateau freshwater lake in Yunnan Province, has experienced algal bloom events frequently in recent years. To understand the spatial and temporal variation pattern of algal bloom and to find the key driving factors, we divided the Waihai, Lake Dianchi into three zones (north, middle and south) according to the water quality monitoring points, and extracted algal bloom information from remote sensing images (Moderate Resolution Imaging Spectroradiometer, MODIS) for Waihai, Lake Dianchi during 2002-2018. Based on the hydrological and meteorological data in 2007-2018, Aquatic Ecosystem Model-3 Dimensional (AEM3D) was set up to calculate water residence time at the north, middle and south zones of Waihai, Lake Dianchi. Redundancy analysis (RDA), Random Forest (RF) and Spearman correlation analysis methods were adopted to identify the key driving factors for algal blooms at the north, middle and south zones of Waihai, Lake Dianchi. The results showed that the ratio of algal bloom area to the whole area at Waihai gradually decreased with obvious seasonality and spatiality with the largest ratio value in autumn mainly during 2002-2018. In the three zones, the ratio of algal bloom area to the zone area followed a spatial pattern of north > middle > south. At each zone, the ratio at the east was larger than that at the west in the north zone, whereas there was a reversed spatial distribution pattern for the middle and south zones of Waihai. The statistical analysis of meteorological and water quality factors with response factors (proportion of algal bloom area and chlorophyll a) showed that wind speed, water temperature and sunshine duration were the main driving factors of algal blooms for Waihai of Lake Dianchi. During the algal bloom period, as the speed of wind increased, the proportion of algal bloom area at the north, middle and south zones of Waihai showed a decreasing trend and the wind from southwest was the dominant direction. At the three zones, water residence time was positively correlated with algal bloom area and gradually increased from north to south. The water residence time at the west was longer than that at the east in the north zone, whereas there was no significant difference between the west and east in terms of the middle and south zones of Waihai. Wind speed and wind direction were the main factors affecting spatial variation and algal bloom area.