Objective To analyse clinical information from a cohort of 877 cochlear implant (CI) surgeries performed in patients with inner ear malformations and report our experience with this procedure. Methods Clinical information on patients with inner ear malformation who underwent CI surgery in our department from January 2010 to April 2017 was analysed. Results Seven hundred and fifty-four CI surgeries (86.0%) were uneventful but cerebrospinal fluid gusher occurred during surgery in 118 cases (13.5%). Not including the patients lost to follow-up, postoperative Categories of Auditory Performance (CAP) and Speech Intelligibility Rating (SIR) scores were collected from 13 patients with common cavity deformity, 38 with IP-I, 11 with hypoplasia, 13 with IP-III, 285 with IP-II and 43 with cochlear nerve deficiency. The mean CAP scores were 2.55, 3.39, 3.45, 3.77, 3.98, 2.95 and 2.90, and the mean SIR scores were 1.54, 3.68, 3.72, 3.54, 3.80, 2.31 and 2.32. Patients with common cavity deformity who underwent surgery using the traditional facial recess approach or transmastoid slotted labyrinthotomy approach had significantly better post-activation scores on the CAP, SIR and Meaningful Auditory Integration Scale/Infant-Toddler Meaningful Auditory Integration Scale, with no significant differences between the two approaches. Conclusion The traditional facial recess approach can be successful, and several approaches may be used for electrode insertion and gusher control in patients with a severe deformity, particularly common cavity deformity and IP-III. A gusher was the most common intraoperative finding and occurred most often in patients with IP-III. Careful consideration of the type of electrode used is important.