Paleoclimatic records from the East Asian summer monsoon (EASM) margin are regarded as a direct reflection of the intensity and northern extent of the EASM. Here, we focus on reconstructing climatic evolution over the past 1800 years from two alkaline lakes, Chagan Nuur and Sangin Dalai Nuur, in southern Inner Mongolia. With age control provided by 13 Accelerator Mass Spectrometry radiocarbon ages and ²¹⁰Pb/¹³⁷Cs dating, analyses of grain size, X-ray diffraction, magnetic susceptibility, carbonate content, total nitrogen, total organic carbon and the stable isotopic composition of carbon (δ¹³C) and nitrogen (δ¹⁵N) in sedimentary organic matter and calculation of organic carbon to nitrogen atomic ratios have been performed to investigate hydrodynamic processes, ecological conditions and corresponding lake-level fluctuations, in response to climate change. Our results show that the lake level of Changan Nuur frequently fluctuated since 546 CE, with four centennial-scale intervals of lake expansion at around 755, 1178, 1350 CE, and after 1950 CE, and one interval of lake recession from 1593 to 1782 CE. Sangin Dalai Nuur experienced mainly low-amplitude lake-level fluctuations since 212 CE, except for severe lake shrinkage from 1417 to 1872 CE. A regional comparison shows that three warm and humid intervals (640–800 CE, 1088–1288 CE, and after 1950 CE) and one cold and dry interval (1417–1872 CE) recognized from our records could correspond to the Sui-Tang Warm Period, the Medieval Climate Anomaly, the Current Warm Period and the Little Ice Age, respectively. Moreover, our results are roughly synchronous with moisture conditions revealed by proxy records from monsoonal northern China, demonstrating that the highly variable lake levels and climatic conditions in southern Inner Mongolia were controlled by centennial-scale variations in EASM over the past 1800 years.