Animal vocalizations and human speech are typically characterized by a complex spectrotemporal structure, composed of multiple harmonics, and patterned as temporally organized sequences. However, auditory research often employed simple artificial acoustic stimuli or their combinations. Here we addressed the question of whether the neuronal responses to natural echolocation call sequences can be predicted by manipulated sequences of incomplete constituents at the midbrain inferior colliculus (IC). We characterized the extracellular single-unit activity of IC neurons in the great roundleaf bat, Hipposideros armiger (both sexes), using natural call sequences, various manipulated sequences of incomplete vocalizations, and pure tones. We report that approximately two-thirds of IC neurons exhibited a harmonic interaction. Neurons with high harmonic interactions exhibited greater selectivity to natural call sequences, and the degree of harmonic interaction was robust to the natural amplitude variations between call harmonics. For 81% of the IC neurons, the responses to the natural echolocation call sequence could not be predicted by altered sequences of missing call components. Surprisingly, nearly 70% of the neurons that showed a harmonic interaction were characterized by a single excitatory response peak as revealed by pure tones. Our results suggest that prevalent harmonic processing has already emerged in the auditory midbrain IC in the echolocating bat.