The invention discloses a method and a system for automatically generating a value-added tax invoice voucher. The method comprises the following steps: acquiring invoice data in a value-added tax invoice of an invoice voucher to be generated; Determining accounting systems set by an enterprise, and determining subject types corresponding to the value-added tax invoice generation invoice certificates according to subject types corresponding to different accounting systems in a preset subject comparison relationship; And generating an invoice voucher of the value-added tax invoice according to avoucher generation rule by using invoice information in the value-added tax invoice and the subject type corresponding to the generated invoice voucher. According to different accounting systems andthe types of the value-added tax invoices, the value-added tax invoices are stored; setting an invoice certificate generation rule; The voucher is automatically generated by obtaining the related information in the value-added tax invoice, the enterprise account-making efficiency is greatly improved, meanwhile, the accuracy of generating the voucher to obtain the subject is ensured according to the set subject comparison relationship, the problem that an accountant repeatedly and manually selects the subject and inputs the subject amount is solved, and the working efficiency is improved.