The invention discloses a file multi-encryption two-dimensional code electronic encryption and decryption management system and method, which apply a multi-information encryption two-dimensional codeanti-counterfeiting technology to realize electronic anti-counterfeiting of secret-related files and solve the security problem of storage and transmission of the secret-related files. A public key encryption and private key decryption mode is established, and the private key encryption and public key combination mode forms a complete anti-counterfeiting and identification system. The secret-related file is subjected to asymmetric encryption, the encrypted file is analyzed, decomposed and recoded through the file byte code processing technology, the two-dimensional code serves as a carrier, electronic anti-counterfeiting of the secret-related file is achieved, and the safety problem of storage and transmission of the secret-related file is solved. By constructing a matched management application system, a management mode of manual and technical integration, transceiving management of secret-related files, operation and maintenance management of a secret-related information system and the like are realized, innovation is realized on thinking, ideas and methods, and the management capability and the management effect of the secret-related files of the institutions are further improved.