The important strategy decision making system, one of the difficult problems of the research of Group Decision Support System, is an open complex huge system, which is almost non structure and hard to construct. In order to organize and take advantage of decision making departments more effectively, this paper presents the thought of combining Multi Agent System with Dynamical Alliance and set up the GDSS Framework of Organization Oriented Dynamic Alliance based on Multi Agent after analyzing the characteristics of MAS and Dynamical Alliance. Different departments can be organized more effectively on the three layer system structure composed of the strategy layer, the tactics layer and the operation layer. The decision making layer of each department is composed of the integrate decision making subsystem, which means that the decision making layer of each department can be used solely or be a part of Dynamic Alliance to make the important strategy decision and the system gets more flexible.