The invention discloses a stock right registration transaction system building method based on an alliance chain, and the method takes the alliance chain as the technical support. Combined with the conventional laws and regulations, the method provides a brand new stock right digitalization unique certificate. Different from a centralized central registration settlement mechanism, the system employs a distributed technical configuration, and all participants jointly maintain a stock right registration and transaction account book, thereby guaranteeing the public transparent and real and reliable stock right registration and transaction, effectively reducing the credit risks of transaction, avoiding the maintenance of a paper stock transfer book, and greatly improving the stock right registration and transaction efficiency. In addition, the method enables the block chain technology to be used in the field of stock right transaction business for the first time, builds a unified and standard stock right transaction platform, achieves the digitalized management of the stock rights, can effectively prevent the credit risks of stock right transaction, improves the transaction and supervision efficiency, and reduces the transaction cost.