Polycyclic aromatic hydrocarbons (PAHs) have strong carcinogenicity, teratogenicity, mutagenicity and other adverse effects on human beings. They are one of the most dangerous pollutants, which have attracted great attention in the past decades. In this work, aiming at the actual problems that water environment is polluted and human health is threatened by PAHs, surface enhanced Raman spectroscopy (SERS) combined with Random Forest (RF) calibration models were used to quantitative analysis of phenanthrene and fluoranthene in water. Firstly, the SERS data was collected after samples mixed with Ag NPs, after 31 PAHs samples were prepared. Secondly, it was discussed how spectral preprocessing integration strategies affect on the prediction performance of the RF calibration models. And then, the effect of mutual information (MI) variable selection method on the performance of RF calibration models was explored. Finally, the RF calibration models were established for phenanthrene and fluoranthene. For the prediction set, a lowest mean relative error (MRE) and a largest determination coefficient (R2) were obtained. For quantitative analysis of phenanthrene, the final prediction performance results show that R2p is 0.9780, and MREp is 0.0369 based on the D1st-WT-RF calibration model. For fluoranthene, WT-D1st-MI-RF is a better calibration model, and corresponding to R2p and MREp are 0.9770 and 0.0694, respectively. Hence, a rapid and accurate quantitative method of PAHs is established for the real-time detection of water environmental pollution, which is intended to provide new ideas and methods for the quantitative analysis of PAHs in water.