Phenanthrene (PHE) is a typical food chain biomagnified compound which endangers human health and is generally accumulated from marine lives. Previous PHE-stressed Carp acute toxicity test showed that the safe concentration of PHE to carp was 1.12 mg/L. In this study, the carp was long-term exposed to PHE below safe concentration up to 25 days. The gene expression levels and cytochrome P450 (CYP1A/EROD (7-Ethoxylesorufin O-deethylase)) and glutathione S-transferase (GST) activities were determined in the carp liver and brain tissues. The results showed that both the CYP1A mRNA expression and EROD activity in the liver were continuously stimulated after induction with the increase in exposure time and exposure concentration. However, with the increase of PHE concentration, GST mRNA expression in the liver was firstly induced and then inhibited and the induction was significant in the treatment with 0.1 mg/L PHE in the 15th day (almost 2-fold). In the brain, after the 15th day, GST mRNA expression was suppressed, but GST activity was induced. Correlation analysis results showed that the CYP1A mRNA expression was significantly correlated with the activity of EROD in both tissues (liver, r = 0.602, P < 0.01; brain, r = 0.508, P < 0.01), but the correlation between GST mRNA expression and GST activity was poor (liver, r = 0.385, P < 0.01; brain, r = 0.293, P < 0.01). This experiment revealed the self-regulation mechanism of carp exposed to lower than safe concentrations of PHE for a long time, indicating the toxicological risk of PHE in the ecosystem.