A control system and method thereof for secure manufacturing, comprising a source end, a verification end, and a production end. Providing a source file, the source end encrypting and signing the source file to generate a transfer file and to generate an authorization information simultaneously, the transfer file being transferred to the production end, and the authorization information being transferred to the verification end. After the production end is authorized by the verification end, the transfer file is verified and decrypted, and can be re-encrypted or not re-encrypted to be written into a product or to generate a product.