Reservoir sediment is a major player in the terrestrial carbon (C) budget, and the quantification of C burial in sediments is important in assessing the reservoir’s role in the global C budget. However, assessments of C burial in sediments of sub-tropical hydroelectric reservoirs and their potential as C sinks are thus far limited due to a lack of whole reservoir assessments of C burial. In this study, a combined seismic survey with sediment core analysis was conducted in the Xin’anjiang Reservoir, the first large hydroelectric reservoir in China. The total organic carbon (TOC), total nitrogen, isotopic C composition (δ13C), and sediment grain size were analyzed. 210Pb and 137Cs were used to obtain the sediment chronologies. The data suggest that bottom bathymetry of the pre-existing reservoir is an important factor on sediment accumulated within the reservoir. The sediment OC content and trophic state became controlling factors and accelerated the OC burial in the sediment. Based on the interpolated sediment thickness data and total reservoir area, the average TOC burial rate was estimated at 34.0 g C m−2 year−1 (ranging 0–676.7 g C m−2 year−1). This rate is within that estimated by sediment coring (mean 40.4 g C m−2 year−1, ranging 15.8–110.1 g C m−2 year−1) as a result of high heterogeneity of sediment distribution and irregular sedimentation. However, the result was close to the estimates of previous studies, demonstrating that the combined method here can also be an effective way to conduct future estimation of C burial in freshwater reservoirs.