Aiming at the loading imbalance of subdomain controller on multi-domain deployment in SDN, based on genetic migrating population and the ideas of migrating switch, this paper has proposed the load balancing mechanism for multi-domain controller in SDN. It integrates main network overheads and designs the optimal migration domain selecting algorithm according to the biological genetic thought, getting the optimal immigration and emigration domain. At the same time, contrasting with the phenomenon of population migration, this paper designs the competition and migrating algorithm for switch based on survival time and elimination mechanism, which balances the number of switches for each subdomain. Compared with the existing algorithm, the simulation shows that the process of migration domain has been significantly optimized. Moreover, it balances the control overheads in subdomain and effectively ensures the balanced distribution of the controller loads.