The invention discloses a medical block chain-based payment system and method. In the blockchain payment system, a patient party, a hospital party and a bank party are respectively a node on the blockchain; Information flow, the capital flow and the medicine flow between three parties form an electronic payment system closed loop; a decentralized block chain public chain is set; nodes participating in the system are freely accessed according to the system specification; in a Data layer, a Data block, a Chain type structure, a Hash algorithm, a Merkel tree and a timestamp mechanism are used for storing each piece of payment transaction data and ensuring the safety of data transaction information by using an asymmetric encryption technology; In the network layer, a peer-to-peer network isadopted to organize nodes to dispersedly participate in verification and accounting of transaction data of each time of payment, in the consensus layer, a POS consensus mechanism is adopted, 1% of transaction amount is adopted as a reward to give accounting nodes in the incentive layer, and in the contract layer, intelligent contracts are packaged in the contract layer, so that the advantages of safe, efficient and convenient payment are achieved.