Aimed at the distributed chilling demand of next generation marine electric propulsion plants, the self-reconfiguration and self-healing problem of marine central cooling system, a multi-agent autonomous control framework for a certain type of central cooling system was proposed. The specific structure of individual agent and systematic configuration of agent group was designed. The agent alliance and acquaintance mechanism was adopted to improve contract net cooperation model. The cooperation process of multi-agent system during task allocation and fault recovery was optimized. On this basis, a prototypical apparatus of the central cooling system was designed, the experimental research platform for multi-agent autonomous control system was built, and the performance analysis and verify of control system was carried out. The results show that the designed multi-agent autonomous control architecture implements dynamic reconfiguration and fault recovery process autonomously, and enable marine central cooling system to have the ability of selfreconfiguration and selfhealing.