Cholesterol granuloma of the middle ear is frequently observed in patients with otitis media with effusion but has never been reported in a patients with middle ear malformation. Our patient, a 21-year-old woman, had severe middle ear cholesterol granuloma extending from the mastoid cells to the eardrum and through the epitympanum, mesotympanum, and hypotympanum. Early operation was required to rule out neoplasms, such as glomus tumor; venous anomaly; and cholesteatoma, since the initial symptoms were rapidly deteriorating hearing ability with continuous bloody ear discharge. The malleus head and incus body were located near the aditus ad antrum, and the chorda tympanic nerve, which is usually located between the malleus handle and the long process of the incus, was anomalously located across the middle tympanic cavity. The severe cholesterol granuloma was considered to have arisen from bleeding from a small vein near the chorda tympanic nerve, narrowed aditus ad antrum combined with the anomalous locations of the malleus head and incus body, and disturbed function of the auditory tube with otitis media with effusion. This severe cholesterol granuloma was treated with intact canal wall staged tympanoplasty of type III with mastoid obliteration.