Research on the holism of complex systems,especialy the emergence of holism is an importment and hard subject in moder scientific research.The attemp to use multiagents,even adaptive multiagents to analyse system holism is not proper in system methodology.The paper starts from the basic concepts of holism and emergence of complex systems,points out the analysis method for holism,and gives the overall multiagent framework based on holism.By discussing the diffierences and relations of holism and emergence,we declare that mathematics,logic and experimentation (simulation) can be used in holism analysis.Finally,we give the multiagent reference architecture based on holism for analysing the holism and emergence of complex systems.