Cross-shelf transport of particulate organic carbon (POC) is an essential but poorly quantified process regulating the POC flux and the biological pump efficiency in marginal seas. Here, we estimated the cross-shelf export flux of 234Th and POC from the northern South China Sea (NSCS) shelf based on a dataset of 234Th in the water column and the underlying sediments over the shelf (bottom depth ≤ 200 m) and the adjacent slope (bottom depth > 200 m). Based on a full mass balance of 234Th throughout the water column and the underlying sediments, we found that besides radioactive production and decay, sedimentary accumulation and cross-shelf export associated with drifting particles were the most important processes in the 234Th budget. The input via horizontal shelf-slope water exchange and along-shelf water transport was a 234Th source to the shelf water, and neglecting this component would underestimate the actual vertical 234Th and POC fluxes by ~10–33%. The POC flux via vertical export from the euphotic zone was 26 ± 1 mmol m−2 d−1 while that via cross-shelf transport was 9.9 ± 3.4 mmol m−2 d−1. The cross-shelf exported POC presumably inject into the intermediate/deep waters and could be trapped for several decades in the SCS. Our results highlight the importance of cross-shelf POC transport in regulating carbon storage in the SCS on seasonal to longer time scales. A compilation of the case studies regarding cross-shelf transport suggests its role in the carbon cycle might be more important than previously recognized and needs to be re-evaluated.