The invention provides a multifunctional invoice management method. The multifunctional invoice management method includes S1, recognizing identities; S2, purchasing invoices; S3, selecting issuing modes of the invoices; S4, recording data information of the invoices; S5, encrypting recorded data of the invoices; S6, printing the invoices; S7, decrypting data in password regions to completely authenticate the invoices; S8, implementing deduction functions of the value-added tax invoices. The invention further provides a multifunctional invoice management system. The multifunctional invoice management system comprises an invoice source control unit, an identity recognition unit, an invoice issuing unit, an encryption unit, a printing unit, an authentication unit and a deduction unit. The invoice source control unit is used for verifying the authenticity of the paper invoices; the identity recognition unit is used for recognizing identity information of invoice issuing parties; the invoice issuing unit is used for recording the data information of the invoices and issuing the invoices; the encryption unit is used for encrypting the issued invoices; the encrypted invoices can be printed by the printing unit; the encrypted invoices can be decrypted and bidirectionally authenticated by the authentication unit; the deduction unit is used for carrying out deduction on the value-added invoices.