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Isotopic compositions of coeval sulfide and sulfate have been widely employed to reconstruct the seawater chemistry evolution over geologic time; however, these signals can be modulated by other factors, such as the sedimentation rate. Here, we present a data set of pyrite sulfur isotopes (δ34Spy) derived from 60-m drilled core sediments deposited on the inner shelf of the East China Sea since 16.5 ka. The resulting δ34Spy values range from −38.2 to 15.0‰ (Vienna Canyon Diablo Troilite; V-CDT), representing a range of 53.2‰. Freshwater deposition before 12.3 ka produced a limited pyrite abundance and δ34Spy values that fall within the typical range of freshwater environments. After the marine incursion in the study area at 12.3 ka, variations in the δ34Spy values become significantly correlated with sedimentation rates (SRs; r = 0.78, p 0‰), suggesting that SRs exert controls on δ34Spy values. We propose that these sedimentary controls are expressed by modulating the connectivity between porewaters and the overlying seawater. Low SRs tend to form an open diagenetic system, in which the pyrites are able to preserve the large biological fractionations associated with microbial sulfate reduction (and disproportionation). In contrast, high SRs favour a restricted diagenetic system, in which the distillation of porewater sulfate produces pyrites enriched in 34S, masking the magnitude of biological fractionation during microbial sulfur cycling. These findings highlight the critical effect of the local sedimentation regime on pyrite sulfur isotopic compositions, especially within shallow depositional environments, over geologic time.