The invention discloses a control method and system for eliminating inter-domain route path inconsistency. The method comprises the following steps: obtaining a message of an inlet or outlet exchange of an upstream autonomous domain; constructing a new route for the message in the autonomous domain, and feeding the new path to the upstream autonomous domain; the upstream autonomous domain checking the new route, and generating a flow item corresponding to the new route; and issuing the flow item to an exchange occurring in the new route so as to lock an inter-domain route path. According to the invention, the problem of autonomous inter-domain route path inconsistency can be effectively eliminated, the new route is constructed according to an upstream data flow through a downstream autonomous domain, the new route takes influences exerted by the new route on automation of an autonomous domain and also can guarantee that the new route does not cause great route oscillation, an inter-domain route relation can be better reflected, and the application prospect is good.