The driving force of climate change in the monsoon margin is complex, making it a key area for regional and global climate change research. Palaeohydrological studies in the monsoon margin have increased the resolution of research in the long term, transitioning from qualitative to quantitative studies to comprehend climate change processes, patterns, and mechanisms. Testate amoebae (TA) in peat sediments are used as a proxy indicator organism for quantitative reconstruction of palaeohydrology. Thus, their community changes are directly related to precipitation, and widely used to reconstruct the patterns of summer precipitation globally. We investigated TA species and reconstructed palaeohydrological changes in the Greater Khingan Mountains’ Hongtu (HT) peatland, located in the East Asian Summer Monsoon (EASM) margin. The result showed that the most abundant TA species were Assulina muscorum (12.4 ± 5.0%) and Nebela tincta (8.9 ± 4.9%) in the HT peat core. The increase in dry indicator species (e.g., A. muscorum and Alabasta militaris) indicated a drying pattern in the HT peatland since 150 cal yr BP. Principal component analysis (PCA) explained 47.6% of the variation in the selected TA assemblages. During 400 to 250 cal yr BP, PCA axis 1 scores ranged from 0.2 to −1.3 (reflecting a drier climate), associating with the Little Ice Age. The paleohydrology of the northern part of the Greater Khingan Mountains was mainly controlled by the EASM, which was associated with changes in North Atlantic Sea surface temperature and solar radiative forcing. The apparent drying pattern may be the result of the gradual intensification of anthropogenic activities and the increase in EASM intensity.