Provided are a system and method for coping with encrypted harmful traffic in hybrid IPv4/IPv6 networks. The system includes: an encryption key manager collecting encryption key information from a user terminal connected to the hybrid IPv4/IPv6 networks, and storing and managing the information in an encryption key database; an encryption traffic collector collecting encrypted traffic from traffic in the hybrid IPv4/IPv6 networks; an encryption key searcher searching for an encryption key used to decrypt the encrypted traffic from the encryption key database using a source IP address and a destination IP address of the encrypted traffic; a harmful traffic determiner decrypting the encrypted traffic using the encryption key and determining whether the decrypted traffic is harmful traffic; and an encryption traffic processor, if the decrypted traffic is determined to be harmful traffic, blocking the harmful traffic and, if the decrypted traffic is determined to be normal traffic, encrypting the normal traffic, and transferring the encrypted traffic to a user terminal corresponding to the destination IP address, thereby detecting and blocking an attack pattern using the encrypted harmful traffic in hybrid IPv4/IPv6 networks which cannot be detected by a conventional firewall system and more effectively protecting the networks.