Reports of decimeter-scale eukaryotic fossils and oxygenation events in the Gaoyuzhuang Formation (similar to 1.56 Ga, North China Craton) have provided valuable insight into potential links between life and the environment during the early Mesoproterozoic. However, the detailed nature of this relationship remains unclear, partly due to a limited basin-wide stratigraphic framework. Here, we present high-resolution carbon isotope compositions for carbonate and organic matter (delta C-13(carb) and delta C-13(org)) in two fossil-hosting sections, representing shallow and deeper water settings, to calibrate the timing of marine oxygenation and eukaryotic evolution, and to reveal coeval carbon cycle dynamics. Our high-resolution data display a dynamic delta C-13(carb) pattern with four perturbations in Gaoyuzhuang members III-IV, and suggest a causal link between oxygenation and eukaryotic evolution during the second perturbation. The delta C-13(carb) values exhibit a narrow range, but a distinct similar to 2.5 parts per thousand isotopic gradient exists between shallow and deeper water during the third perturbation. By contrast, delta C-13(org) values reflect a more stable, but larger, isotopic gradient (similar to 7 parts per thousand), implying decoupling of the carbon isotopic system. We propose that the delta C-13(org) compositions of shallow and deeper waters were controlled by specific microbial communities in a redox-stratified water column and a larger deep-ocean DOC reservoir, whereas delta C-13(carb) sensitivity was buffered by a large DIC reservoir. Our modeling also highlights that the coeval oxygenation events were able to drive the observed short-term delta C-13(carb) gradient during the third perturbation. Our findings reveal a direct relationship between environmental change and eukaryotic evolution, with implications for understanding Mesoproterozoic carbon cycle dynamics and paleo-redox conditions.