The present study was aimed to evaluate the protective effects of six different polyphenols against benzo(a)pyrene (BaP)-induced cytotoxicity in Caco-2 cells. The results shows that treatment of quinic acid, ferulic acid, homovanillic acid and BaP decreased the cell viability, whereas only co-treatment of 20 µM eriodictyol and naringenin reduced BaP-induced cytotoxicity, including cell apoptosis, cell cycle change and oxidative stress. Moreover, all results show that the inhibitory effect of eriodictyol was better than that of naringenin. Further, the potential protective mechanism of eriodictyol against BaP-induced toxicity was investigated by proteomics. We found that the genetic information processing pathway involves in 80 differentially expressed proteins (DEPs) showed the highest proportion and number of total proteins. Finally, eriodictyol inhibited BaP-induced cytotoxicity by regulating the expression of key proteins such as RPA2, SNRPA, RAD23B, NUP155 and AARS in transcription and translation. Overall, our results provide a new perspective for polyphenols inhibiting BaP-induced carcinogenesis.