Wide Area Protection System (WAPS) undertakes the important task of maintaining system reliability and stability when the power system is subject to abnormal or predetermined unstable conditions. The existing WAPS adopts a centralized mechanism to record and audit communication messages, which faces the risk of excessive authority and tampering with communication records and audit logs, thus making it impossible to achieve true transparency and fairness. Due to the involvement of multiple parties and equipment maintained by different manufacturers in the communication of WAPS, there are difficulties in tracing the cause of the accident and determining the at-fault party following misoperations and miss trips. To address this issue, we propose a semi-centralized blockchain system with multi-chain for auditing communications of WAPS. We first propose a semi-centralized system architecture according to the system architecture and management requirements of WAPS. Then, we utilize the blockchain network as a self-recording channel to achieve tamper-proof and non-repudiation verification interaction. We also design a multi-chain structure and classification node mechanism to meet the communication auditing requirements of multiple WAPS. We have designed a new block structure that conforms to the communication protocol of WAPS. To reduce the storage burden caused by the ever-expanding blockchain ledger, we propose a deletable blockchain scheme while maintaining the integrity and security of blockchain. Analysis and experiments show that the proposed blockchain system can support the secure, transparent, tamper-proof and traceable communication recording and auditing of WAPS along with high performance.