With increasing stress posed to the marine ecosystem and coastal communities, prevention and control of coastal pollution becomes urgent and important, in which the identification of pollution sources is essential. Currently, the pollutant source apportionment in coastal areas is mainly based on receptor models, such as the positive matrix factorization (PMF) model. Nevertheless, these models still lack consideration of the changes of pollutant behaviors (e.g., the degradation of pollutants) which cause the differences in pollutant compositions. Subsequently, the source apportionment via receptor models only based on the monitoring data may not be consistent with the one in pollution sources. To fill this gap, a pollutant degradation model was firstly developed in this study. Accordingly, the degradation model was inversed to estimate the pollutant concentrations at their emitting sources, based on the monitoring concentration in the coastal area. Finally, the estimated concentrations were fed to the PMF model for pollutant source apportionment, advancing the PMF model with degradation process. To demonstrate the feasibility and accuracy of the developed model, a case study of source appointment was carried out based on the polycyclic aromatic hydrocarbons (PAHs) in the sediments of the Pearl River Estuary. The results indicated the same types of emission source identified by the original and advanced PMF models, which were oil spill, biomass and coal combustion, and traffic emission. Nevertheless, the contributions of sources were significantly varied between the two models. According to the analyses based on emission inventory, the offsets of the results from the original PMF model were −55.4%, 22.7%, and 42.2% for the emission sources of oil spill, biomass and coal combustion, and traffic emission, respectively. Comparatively, the offsets for the advanced PMF model narrowed down to −27.5%, 18.4%, and −4.4%. Therefore, the advanced PMF model is able to provide satisfactory source apportionment for organic pollutants in coastal areas, and thus further provide a scientific basis for marine pollution prevention and control.