The invention discloses an invoice certification system supporting multiple invoice types. The system comprises the scanning equipment, an image identification module, an invoice type determination module, a two-dimensional decoding processing module, a decryption module, a comparison module and a certification result input module. The invention further discloses an invoice certification method supporting multiple invoice types. Through the method and the system, not only can work burdens of the staff in a working hall be reduced, but also the certification time of taxpayers can be further saved.