Since low flexibility and non-dynamic problems exit in the process of software system integration, a MultiAgent System frame model which introduces the agent techniques into system integration domain is proposed for problem solving. Based on the MAS frame model, independent software units are wrapped to agents, and their integration logic is described by the script language. Through explaining the file, the collaboration of multi-agent is under control. Dialogue Expansion Contract Net Protocol is used for the cooperation when agent cannot solve problems by itself. In order to achieve the aim of flexible and dynamic integration, new wrapped agents can be added into MAS dynamically and the edited script can be explained by the parser. Finally, the Agent-based System Integration Tools is built upon this frame model, and an application of this model about the Border and Coast Defense System is presented, which verifies the rationality, feasibility and efficiency.