Several main metabolites of benzo[a]pyrene (BaP) formed by Penicillium chrysogenum, Benzo[a]pyrene-1,6-quinone (BP 1,6-quinone), trans-7,8-dihydroxy-7,8-dihydrobenzo[a]pyrene (BP 7,8-diol), 3-hydroxybenzo[a]pyrene (3-OHBP), were identified by high-performance liquid chromatography (HPLC). The three metabolites were liable to be accumulated and were hardly further metabolized because of their toxicity to microorganisms. However, their further degradation was essential for the complete degradation of BaP. To enhance their degradation, two methods, degradation by coupling Penicillium chrysogenum with KMnO4 and degradation only by Penicillium chrysogenum, were compared; Meanwhile, the parameters of degradation in the superior method were optimized. The results showed that (1) the method of coupling Penicillium chrysogenum with KMnO4 was better and was the first method to be used in the degradation of BaP and its metabolites; (2) the metabolite, BP 1,6-quinone was the most liable to be accumulated in pure cultures; (3) the effect of degradation was the best when the concentration of KMnO4 in the cultures was 0.01% (w/v), concentration of the three compounds was 5 mg/L and pH was 6.2. Based on the experimental results, a novel concept with regard to the bioremediation of BaP-contaminated environment was discussed, considering the influence on environmental toxicity of the accumulated metabolites.