Recently, security issues such as identity authentication and digital signatures in industrial control systems have received more and more attention. This study introduces the decentralized certificateless (CFL) cryptography authentication system into the identity authentication of the industrial control system and proposes a signature authentication scheme for the industrial control system based on CFL. It builds the CFL-SYS authentication model for the industrial control system based on the CFL authentication system and introduces UKey as the certificated carrier to decentralize the signature verification process. A random private key and a flagging private key are generated by calculating the hash value of the user ID to realize one-person-one-key encryption, which satisfies the user’s private ownership of the private keys and protects the user’s privacy. Theoretical analysis and experimental results show that the proposed scheme can meet the millisecond-level application requirements in terms of throughput and system verification response time, and can provide an autonomous, reliable, and efficient signature authentication scheme for large-scale industrial control systems.