The global climate during the latest Cretaceous became variable, with several global warming and cooling trends in a context of a greenhouse Earth. The responses of marine ecosystems to these climate events are relatively well known worldwide; however, lacustrine responses are poorly known due to the less frequent and discontinuous terrestrial fossil records. The relative changes in charophyte diversity in continuous lacustrine sedimentary sequences from two basins in East Asia, i.e., Songliao and Jiaolai, are considered here for the first time to establish their correlation with global climate changes during the Late Cretaceous and K/Pg boundary, compared with the well-studied south European Ibero-Armorican Island. Lacustrine deposits correlated with the Campanian-Maastrichtian Boundary Event (CMBE), related to a long cooling period provided a relatively low diversity in East Asia. In contrast, we detected a diverse charophyte flora in lacustrine deposits correlated with the Mid-Maastrichtian Event (MME) in East Asia in a global warming trend. A higher charophyte diversity was further found in the end-Cretaceous global warming event due to speciation under the background of latest Maastrichtian warming event (LMWE). During the LMWE, Characeae species such as Microchara cristata reduced its size significantly due to environmental stress probably related to the Deccan volcanism. On the other hand, a general tendency of increasing the gyrogonite size in new Characeae taxa has been detected in populations extracted from lower Danian deposits, probably related to stable palaeoenvironmental conditions in a global cooling context. This study represents the first attempt to correlate the response of the charophyte flora to global climate changes in permanent lacustrine systems during the three main Late Cretaceous-early Danian climatic turnovers.