Abstract: Glycerol dialkyl glycerol tetraethers (GDGTs), an emerging class of biomarkers, have been widely applied in studies of marginal sea sedimentary records and environmental evolution due to their significant advantages in indicating the sources of organic matter, reconstructing sea surface temperature (SST) during geological periods, and reflecting environmental responses to variations in material input. However, the relatively high sedimentation rates in the mud area of the inner shelf of the East China Sea limit long-term investigations of environmentally sensitive muddy sedimentary records. In this study, the ECS1601 core, located at the southern end of the mud area on the inner shelf of the East China Sea, was selected as the research object. By integrating lithological characteristics, stratigraphic chronology, grain-size parameters, and GDGT-related indices, the evolution of the sedimentary environment in this muddy area since Marine Isotope Stage 5 (MIS 5) was investigated. Results show that since MIS 5, the relative contributions of terrestrial and marine organic matter in the study area have been mainly controlled by sea-level fluctuations. During periods of high sea level, the proportion of marine-derived organic matter increased. Meanwhile, the sources of organic matter were also jointly influenced by hydrodynamic conditions driven by the East Asian monsoon and environmental changes within the drainage basin. During the MIS 4, the mean SST fluctuated from 16.38 to 26.66 °C, and the SST exhibited relatively large variability influenced by multiple end-member sources, whereas the SST fluctuations in other stages were comparatively moderate. Meanwhile, the relationship between organic matter composition and the sedimentary environment in the mud area over a long-term timescale (since MIS 5) was also revealed. Our findings provided important evidence for understanding the geological history of the region and global environmental change, and contributed new data to related global comparative studies.