Aim To study the effectiveness of cochlear implantation in deaf children with gene mutation. Method 420 children from three medical centers with cochlear implants were selected. Before wearing the cochlear implant and 6 months after wearing the cochlear implant, the children's rehabilitation efficacy was evaluated through categories of auditory performance (CAP) and speech intelligibility rating (SIR). The SSF-MCDI and MUSS before and after the treatment were also compared. Results The CAP and SIR scores of the children after the intervention were higher than those before the intervention (P < 0.05). Univariate analysis found that the age of cochlear implantation, parents' education level, and monthly family income were all influencing factors of the CAP score of children with prelingual cochlear implantation (P < 0.05). Multivariate logistic regression analysis shows that the age of cochlear implantation <5 years, parents' education level, and monthly household income are all independent risks of CAP scores in children with prelingual deaf cochlear implantation. Univariate analysis found that the age of cochlear implantation, parents' education level, and monthly household income are all based on the SIR scores of children with prelingual cochlear implantation. Multivariate logistic regression analysis can be obtained: the age of cochlear implantation less than 5 years, the education level of parents, and the monthly family income are independent risk factors for SIR scores in children with prelingual deaf cochlear implantation (P < 0.05). Conclusion The rehabilitation effect of cochlear implants is significant, and the age of cochlear implantation, parents' education level, and monthly family income are all related factors that affect the rehabilitation effect.