A system and method for aborting web services automatically. An application program container has a first web service application program embedded, intercepts a message that is transmitted and received between a second web service program located externally and the first web service application program, identifies the kind of an operation requested by the second web service application program, and keeps information required for compensation. A protocol manager generates and manages a first sub-transaction object by a request of the second web service application program. A local compensator compensates the first sub-transaction if a global transaction coordinator sends a command to compensate a second sub-transaction already committed. A protocol service unit transmits and receives messages for managing the first sub-transaction. A registration service unit registers the generated first sub-transaction with the global transaction coordinator.