A 1000-year high-resolution (∼10 years) chironomid record from varved sediments of Sugan Lake, Qaidam Basin on the northern Tibetan Plateau, is presented. The chironomid assemblages are mainly composed of the relatively high-saline-water taxa Psectrocladius barbimanus-type and Orthocladius/Cricotopus, and the relatively low-saline-water taxa Procladius and Psectrocladius sordidellus-type. Variations in the chironomid fauna and inferred salinities suggest that over the last millennium, the Sugan Lake catchment has alternated between contrasting climatic conditions, having a dry climate during the period 990–1550 AD, a relatively humid climate during the Little Ice Age (LIA) (1550–1840 AD), and a dry climate again from 1840 AD onwards. At the decadal to centennial scale, a wet event around 1200–1230 AD, interrupting the generally arid period (990–1550 AD), and a dry event around 1590–1700 AD, punctuating the generally humid period (1550–1840 AD), are clearly documented. Trends in the chironomid-based salinity time series indicate a highly unstable climate during the LIA when salinity fluctuations were of greater magnitude and higher frequency. The effective moisture evolution in the Sugan Lake catchment during the last millennium reconstructed by chironomid analysis is in broad agreement with previous palaeo-moisture data derived from other sites in arid Northwest China (ANC). The LIA, characterized by generally humid conditions over the westerly-dominated ANC was distinctly different from that in monsoonal China, implying an “out-of-phase” relationship between moisture evolution in these two regions during the past 1000 years.