The inter-domain routing system is a complex macrosystem just like the Internet, and the self-organization theory is the efficient utility for studying complex system. This paper analyzes the intrinsic rules and behavioral exhibitions of inter-domain routing system from the view of self-organization, and evaluates the mending methods to BGP protocol for improving the scalability, convergence, stability and security of inter-domain routing system, in order to extract good experience and find out the deficiency. Based on the development forecast of BGP, the rules and techniques of using the self-organization character to solve the inter-domain system problems are presented.