Abstract To localize a seen object, the superior colliculus of the barn owl integrates the visual and auditory localization cues which are accessed from the sensory system of the brain. These cues are formed as visual and auditory maps. The alignment between visual and auditory maps is very important for accurate localization in prey behavior. Blindness or prism wearing may interfere this alignment. The juvenile barn owl could adapt its auditory map to this mismatch after several weeks training. Here we investigate this process by building a computational model of auditory and visual integration in deep Superior Colliculus (SC). The adaptation of the map alignment is based on activity dependent axon developing in Inferior Colliculus (IC). This axon growing process is instructed by an inhibitory network in SC while the strength of the inhibition is adjusted by Spike Timing Dependent Plasticity (STDP). The simulation results of this model are in line with the biological experiment and support the idea that STDP is involved in the alignment of sensory maps. This model also provides a new spiking neuron based mechanism capable of eliminating the disparity in visual and auditory map integration.