The main focus of the present study was to explore the longitudinal changes in the brain executive control system and default mode network after hemispherotomy. Resting-state functional magnetic resonance imaging and diffusion tensor imaging were collected in two children with drug-resistnt epilepsy underwent hemispherotomy. Two patients with different curative effects showed different trajectories of brain connectivity after surgery. The failed hemispherotomy might be due to the fact that the synchrony of epileptic neurons in both hemispheres is preserved by residual neural pathways. Loss of interhemispheric correlations with increased intrahemispheric correlations can be considered as neural marker for evaluating the success of hemispherotomy.