With climate warming and intensification of human activities, the eco-environmental problems of lakes in middle and high latitudes become increasingly prominent. Qinghai Lake, located in the northeastern of the Tibetan Plateau, is the largest inland saltwater lake in China. Recently, the problem of Cladophora blooms has been widely concerning. In this study, the area of floating Cladophora blooms (hereafter FCBs) in Qinghai Lake from 1986 to 2021 was extracted using Floating Algal Index (FAI) method based on Landsat TM/ETM+/OLI and Sentinel-2 MSI images, and then the intra- and inter-annual variation characteristics and spatial patterns of FCBs were analyzed. The results show that the general change trend of FCBs in Qinghai Lake featured starting in May, expanding rapidly from June to August, and increasing steadily from September to October. From 1986 to 2021, the area of FCBs in Qinghai Lake showed an overall increasing trend in all months, with the largest increase in July at 0.1 km2/a, followed by October at 0.096 km2/a. Spatially speaking, the FCBs area showed a significant increasing trend in the northern Buha River estuary (BRN) and southern Buha River estuary (BRS) regions, a slight increase in the Shaliu River estuary (SR) region, and a decreasing trend in the Quanji River estuary (QR) region and the Heima River estuary (HR) region. The correlation between the meteorological factors and the changes in FCBs was weak, but the increase in flooded pastures in the BRN region (Bird Island) due to rising water levels was definitely responsible for the large-scale increase in FCBs in this region. However, the QB, northeastern bay of Shaliu River estuary (SRB) and HR regions, which also have extensive inundated grassland, did not have the same increase in FCBs area, suggesting that the growth of Cladophora is caused by multiple factors. The complex relationships need to be verified by further research. The current control measures have a certain inhibitory effect on the Cladophora bloom in Qinghai Lake because the FCBs area was significantly smaller in 2017–2020 (5.22 km2, 3.32 km2, 4.55 km2 and 2.49 km2), when salvage work was performed, than in 2016 and 2021 (8.67 km2 and 9.14 km2), when no salvage work was performed.