The invention discloses a smart hospital mobile bar code payment settlement method and system, a storage medium and a terminal. The method comprises: a code scanning machine tool reading a payment code of a user mobile terminal and sending payment code information to an intranet server; the intranet server calling a collection component service according to the received payment code information, and completing information updating of a payment state by means of network interaction among a DMZ front-end processor server, a cloud server and a third-party payment mechanism; and the collection component service continuously polling the deduction result service to judge that the payment of the user is completed, and informing the intranet application to enter the next business processing. The scheme of the invention belongs to low-invasion type reconstruction, does not generate service logic change on the existing access system of a hospital, and the method is safe and efficient, improves the convenient management of hospital finance, and more importantly, improves the use experience of convenient medical treatment of a patient user.