Archaea is an important microorganism distributed in the aquatic environmental conditions. To better understand the diversity of archaea in the water supply reservoir, the objective of this work was to evaluate and compare the sediment archaeal quantity and community diversity in three oligotrophic water supply reservoirs (JPR, ZCR and SBYR) using real time quantitative PCR (RT-qPCR) and high-throughput Illumina Miseq Sequencing (IMS) techniques. The results showed that archaeal 16S RNA gene copy per gram sediment were 6.09×10⁴, 6.19×10⁵ and 1.94×10⁵ for JPR, ZCR and SBYR, respectively (P<0.01). Moreover, in total, 40941, 36552 and 31234 effective sequence reads of the sediment archaeal 16S rRNA gene were obtained using Illumina Miseq sequencing method from sediments of the ZC, SBY and JP reservoirs respectively. The highest Chao diversity index was observed in ZC reservoir, which was 2.80 times higher than that of the lowest JP reservoir. Methanosaeta, Methanospirillum, Methanosarcina, Methanobacterium, Methanosphaerula, Methanocella, Methanomethylovorans, Methanocorpusculum, Methanoculleus, Methanolinea, Methanosphaera and Thermofilum were observed in the sediments from three reservoirs. Methanosaeta was the dominated species in ZC and SBY reservoirs, and Methanosarcina was the dominate species in JP reservoir. Thermofilum was only found in JP reservoir. ZC reservoir had significantly greater operational taxonomic unit (OTU) richness. Heat map and principle component analysis (PCA) suggested that there was a distinct different sediment archaeal quantity and community compositions among three water supply reservoirs, which may be play an important role in driving nutrition transportation and shaping the water quality of water supply reservoirs.