The invention discloses an autonomous and cooperated type aircraft cluster system and a running method. The aircraft cluster system mainly comprises at least one node aircraft cluster, wherein the node aircraft cluster has an autonomous running capability and a network information connection function, the node aircraft cluster is provided with a resource sharing interface, node aircrafts in the node aircraft cluster are connected with each other by a space self-organizing network, the node aircrafts in the aircraft cluster fly in shared navigation and cluster flight modes, the commutation is realized by the space self-organizing network, and the fleet configuration is automatically adjusted according to the task existing condition. When the aircraft cluster receives a task instruction, the resource scheduling, the task planning, the task reconfiguration and the failure regrouping are autonomously carried out according to the task types, so as to further complete the tasks. The autonomous and cooperated type aircraft cluster system is suitable for quick or maneuvering launching of small carrier rockets, the quick response of the space system is greatly improved, and the risk of the in-orbit failure of the aircrafts is reduced.