Heteroatom-containing polycyclic aromatic compounds (H-PACs) represent a significant yet frequently overlooked class of organic pollutants in marine environments. This study presents a comprehensive characterization of H-PACs in surface sediments from the China Coastal Seas utilizing a high-throughput screening approach based on comprehensive two-dimensional gas chromatography coupled with high-resolution time-of-flight mass spectrometry (GC×GC-HR-TOFMS). The advanced analytical platform enabled the simultaneous identification and quantification of a diverse range of sulfur-, oxygen-, and nitrogen-containing derivatives that are typically unresolved by conventional methods. Results revealed distinct spatial distribution patterns and compositional profiles across different coastal zones. Furthermore, statistical analyses were employed to elucidate the relationship between H-PAC occurrence and environmental factors, providing critical insights into their sources and fate. These findings highlight the necessity of including H-PACs in routine marine sediment monitoring programs to accurately assess ecological risks.