The development of Software Defined Networking (SDN) provides a completely new design concept for construction of airborne network. For the problem of scalability of control plane in aeronautic swarm, the problem of multi-controller deployment under hybrid hierarchy is studied. First, to realize flexible control of the underlying transport nodes, the local controller resource pool is defined by extending the control hierarchy. Then, to reduce the time complexity and realize rapid deployment of local controllers, the traditional controller deployment is transformed into two steps: sub-domain partitioning and intra-domain deployment. A sub-domain partitioning algorithm based on node density sorting and an in-domain controller deployment algorithm based on improved Pareto simulated annealing are developed. Experimental results show that the proposed algorithm can guarantee load balancing of the controller, and effectively reduce the average delay and average loss rate of network control link. Compared with existing algorithms, the algorithm is more suitable for aeronautic swarm controller deployment in large-scale and dynamic topology environment with less time complexity. © 2018, Press of Chinese Journal of Aeronautics. All right reserved.