The Hirnantian glaciation, which was the first in the Phanerozoic to occur with elevated CO2 levels, caused severe mass extinctions and disrupted biogeochemical cycling in the latest Ordovician. Previous research that aimed at exploring the triggers and consequences (both abiotic and biotic) of this glacial event have largely been based on condensed or incomplete sections. However, there is much debate over the detailed glacio-eustatic processes, and especially over the possible existence and characterization of multiple glacial cycles. Herein we conduct high-resolution geochemical analyses (via XRF core scanning and ICP-OES/MS) and a sedimentological study of three continuous upper Katian - lower Rhuddanian drill cores (Well Huangge-1, Well Shuanghe-1 and Well Yiwan-1), which represent a combination of nearshore and offshore facies in South China. The geochemical and sedimentological evidences reveal for the first time three glacio-eustatic cycles encompassed within a major sea level cycle through the upper Katian and Hirnantian. Each glacio-eustatic cycle comprises a combination of regressive and transgressive systems tracts, with the third one denoting the largest sea level fall and the glacial maximum. This pattern of sea level changes can be correlated with both the glacial sedimentary records and geochemical signals in North Gondwana, Laurentia and Baltica. These glacio-eustatic changes likely led to perturbations in regional marine nutrient cycling and formed a redox landscape that is depicted herein as somewhat different from previous models. We also present the glacio-eustatic effects at a basin scale, and a refined constraint for the tempo of polar ice sheet advances and retreats. It also calls for a re-evaluation of the mechanisms whereby a multi-cycle glaciation led to the Hirnantian biotic crisis, a relationship that may be much more complicated than the simplified cause-and-effect relationship proposed before.