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Autonomic computing system is complex and expected to be self-managing. When designing autonomic computing system, we have to consider its special characteristics. To support the system design, collaborations, and semantic information understanding, this paper proposes a multi-dimensional hierarchical model methodology based on agent-oriented software engineering, to model the system from the design, organization and semantic dimensions. Design model adopts a hierarchical development method based on the component reusability. Organization model mainly study the relation web model to support complex collaborations. And semantic model make use of hierarchical ontology to support heterogeneous resource integration and policy conflicts resolution. The model methodology is efficient and systematic for complex system development.