Pigeons (Columba livia) have excellent flying and orienting abilities and are ideal study subjects for biologists who research the underlying neurological mechanisms that modulate flying and allow birds to find their way home. These mechanisms also attract the engineers who want to apply pigeon locomotion to the design of flying robots. Here, we identified the motor-related brain nuclei and revealed their relationship in spatial distribution in pigeons under light anesthesia and freely moving conditions respectively. Flapping and lateral body movements were successfully elicited when electrical microstimulation was applied to the diencephalon, medial part of the midbrain, and medulla oblongata of lightly anesthetized pigeons (N = 28) whose heads were fixed. The current thresholds for stimulating different nuclei and behavior ranged from 10 μA to 20 μA. During freely moving tests (N = 24), taking off and turning were induced by a wireless stimulator through microelectrodes implanted in specific nuclei or brain regions. The results showed that electrical stimulation of these nuclei elicited the desired motor behavior. In addition, regulatory mechanisms were identified in the motor-related regions and nuclei of pigeons. Overlapping in the behavior elicited by stimulation of different regions indicates that complicated neural networks regulate motor behavior. Therefore, more studies need to be conducted involving simultaneous stimulation at multiple points within the nuclei involved in the networks.