Stable carbon and nitrogen isotopes were measured to analyze trophic level of main waterbirds in Qinghai Lake in May−June, 2008, based on the model of isotopic enrichment and the fractionation factor. Our results indicated that δ15N was significantly enriched in the muscle of waterbirds, but δ13C showed no obvious variation. We obtained a fractionation factor between Gymnocypris przewalskii and Phalacrocorax carbo, i.e., 1.78‰. Phytoplankton, zooplankton, Gammarus suifunensis, G. przewalskii and waterbirds were estimated at the trophic levels of 1.64-2.06, 2.35-2.83, 2.63, 3.64-;4.20 and 3.35-4.93 respectively. P. carbo, Larus ichthyaetus, Larus brunnicephalus and Podiceps cristatus occupied the highest trophic level due to their primary feeding on G. przewalskii. However, Tadorna ferruginea, Sterna hirundo, and Tringa totanus occupied the relatively high trophic levels. Anser indicus, mainly relying on plant materials as their food supply, was at the lowest trophic level. Our results predicted that the future resource situation of G. przewalskii would have great influence on the growth, reproduction and community structure of main waterbirds, especially for P. carbos, L. ichthyaetus, L. brunnicephalus and P. cristatus, consequently on the stability and diversity of the whole ecosystem.