The invention discloses a fusion system for multi-protocol multi-account instant messages and a working method thereof. The system comprises a background server module, a database module and a third party instant messaging server module, wherein the background server module is interconnected with the database module; the output end of the background server module is connected with the third party instant messaging server module; and the background server module comprises a registration module, a logging module, an account binding module, an account adding and deleting module, a friend binding module, a friend unbinding module, a database operating module and a communication module. The work method of the fusion system of the invention comprises a step of registering, a step of logging in a multi-protocol instant messaging tool and a step of updating a contact list. The fusion system and the working method thereof integrate various protocols and various accounts, which is convenient for logging; and simultaneously, the account is convenient for managing so that a instant messaging protocol account supported by a server can be added to a unified registration user name, or a single-protocol account exiting in the unified user name can be deleted randomly.