A novel spacecraft autonomy architecture based on Multi-agent is put forward to fulfill the Self-organization mission planning demands of Multi-spacecraft-coordination.The architecture is divded into Multi-spacecraft-coordination Layer,Spacecraft System Layer and Spacecraft subsystem Layer.The difference of isomorphic spacecraft between heterogeneous spacecraft is analysed,and the model of Multi-spacecraft coordination has been taken.On this basis,bidding mechanism and estimate-publishment mechanisim is designed for the two kind of Multi-spacecraft mission planning,and the algorithm based of SGPlan has been taken.At last,Multi-spacecraft propellant refueling problem was taken as an example,and satisfactory results were obtained through simulation,which shows that the model was reasonable and the algorithm was efficient.The Self-organization mission planning in this article can be refered to real Multi- spacecraft-coordination application.