The concentrations of black carbon (BC) and persistent organic pollutants (POPs) were investigated, based on twenty-five surface sediments sampled from the Jiulong River Estuary and  adjacent Western Taiwan Strait. The correlations between BC and POPs were also discussed. The chemo-thermal oxidation method (CTO-375) and the thermal-optical reflectance (TOR) method were used for BC analysis, while POPs were analyzed by GC-MS and GC-ECD. The results showed that correlations of POPs with BC were associated with the POPs’ sources and the analytical methods for BC. Among the POPs discussed here, polycyclic aromatic hydrocarbons (PAHs) correlated the best with BC, showing a significant correlation (p < 0.01). Organochlorine pesticides (OCPs) showed weak corrlations with BC (p < 0.05). In addition, polychlorinated biphenyls (PCBs) showed the weakest correlation with BC: BC_CTO did not show any correlation  with PCBs, whereas BC_TOR only showed a weak correlation with PCBs (p < 0.05).