The aim of this study is to survey and compare the development of auditory skills in young children with Mondini dysplasia and profoundly-deaf young children with radiologically normal inner ears over a period of 3 years after cochlear implantation. A total of 545 young children (age 7 to 36 months) with prelingual, severe to profound hearing loss participated in this study. All children received cochlear implantation. Based on whether or not there was a Mondini dysplasia as diagnosed with CT scanning, the subjects were divided into 2 groups: (A) 514 young children with radiologically normal inner ears and (B) 31 young children with Mondini dysplasia. The Infant-Toddler Meaningful Auditory Integration Scale (IT-MAIS) was used to assess the children's auditory skills that include vocalization changes, spontaneous alerting to sounds in everyday living environments, and the ability to derive meaning from sounds. The assessment was performed prior to surgery and at 1, 3, 6, 9, 12, 24, and 36 months after implant device switch-on. The mean scores for overall auditory skills were not significantly different between groups A and B at pre-surgery, 1, 12, 24, and 36 months post-surgery, but were significantly different at 3, 6, and 9 months post-surgery. The mean scores for all auditory skills in children with Mondini dysplasia showed significant improvement over time. The mean scores for the three subcategories of auditory skills in children with Mondini dysplasia also showed significant differences at pre-surgery, 1, 3, 6, and 9 months, however, there were no significant differences at 12, 24, and 36 months. Overall, the auditory skills of young children with Mondini dysplasia developed rapidly after cochlear implantation, in a similar manner to that of young children with radiologically normal inner ears. Cochlear implantation is an effective intervention for young children with Mondini dysplasia.