Abstract: Several issues in the information system integration are discussed,such as information integration,function integration,platform integration and human integration etc..A multiphase-based methodology for information system integration is presented,in which the integration is the goal of the system integration,functions integration is the base framework of the system integration,platforms integration is the technological basis of the system integration,and the human integration is the guarantee of the system integration.Based upon the practice of an airline integration information system,a multiphase-based methodology proposed in the paper has illustrated which possesses a theoretical guide for the system integration development.