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The paper concerns the autonomous thermal control system of Nano-satellite with a study of the combination of MEMS (Micro Electro Mechanical Systems)-based efficient cooling technique and the agent-oriented intelligent control strategies issue, especially with the issue of autonomy. The particular interest and complexity are the development of the thermal control system that has the intelligent autonomous control capability to maintain the Nano-satellite optimal performance. Based on the modeling and analysis the dynamic characteristics of efficient cooling system utilizing MEMS-based micro-channel heat sink and micro louver arrays by the means of lumped parameter method, the hierarchical structure of agent-oriented intelligent control method for Nano-satellite autonomous thermal system is investigated. With the domain expert knowledge and Fuzzy reasoning, the innovative agent-oriented intelligent control strategies achieve an autonomous process to regulate several controlled variables according to the expectation of the system situations and variety tendency, the robustness of the thermal control system is accomplished as well.