Organic-mineral interactions are closely linked to the transport and burial of organic matter in dynamic marginal seas. However, identifying these signatures in surface sediments is further complicated by source heterogeneity and hydrodynamic reworking. Here we integrated bulk organic proxies (TOC, TN, and TOC/TN ratios), clay mineral assemblages, and n-alkane proxies to investigate organic-mineral covariation in surface sediments of Bohai Bay (BHB), northern China. The results showed that organic matter in BHB was of mixed terrestrial and marine origin, dominated by terrestrial higher plants, with clay mineral compositions most similar to those of the Yellow River (YR). Both organic and mineral proxies exhibited systematic spatial heterogeneity across the bay. Spearman correlations revealed that TOC content covaried positively with the Carbon Preference Index (CPI) and illite abundance (p ≤ 0.05). Principal component analysis (PCA) explained 57.7% of the variance, with PC1 (35.2%) dominated by the TOC-Illite-CPI association on the positive axis. This pattern is attributed to the prevailing hydrodynamic regime, where coastal currents sort riverine inputs during transport, selectively carrying finer, illite-rich particles offshore. Consequently, this illite-associated terrestrial organic matter is preferentially deposited in the low-energy central bay. The TOC-Illite-CPI coupling provides a useful diagnostic framework for river-dominated marginal seas, offering a new means to disentangle source controls from hydrodynamic sorting effects.