Background Patients with severe profound hearing loss could benefit from cochlear implantation (CI). However, the neural mechanism of such benefit is still unclear. Therefore, we analyzed the electroencephalogram (EEG) and behavioral indicators of auditory function remodeling in patients with CI. Both indicators were sampled at multiple time points after implantation (1, 90, and 180 days). Methods First, the speech perception ability was evaluated with the recording of a list of Chinese words and sentences in 15 healthy controls (HC group) and 10 patients with CI (CI group). EEG data were collected using an oddball paradigm. Then, the characteristics of event-related potentials (ERPs) and mismatch negative (MMN) were compared between the CI group and the HC group. In addition, we analyzed the phase lag indices (PLI) in the CI group and the HC group and calculated the difference in functional connectivity between the two groups at different stages after implantation. Results The behavioral indicator, speech recognition ability, in CI patients improved as the implantation time increased. The MMN analysis showed that CI patients could recognize the difference between standard and deviation stimuli just like the HCs 90 days after cochlear implantation. Comparing the latencies of N1/P2/MMN between the CI group and the HC group, we found that the latency of N1/P2 in CI patients was longer, while the latency of MMN in CI users was shorter. In addition, PLI-based whole-brain functional connectivity (PLI-FC) showed that the difference between the CI group and the HC group mainly exists in electrode pairs between the bilateral auditory area and the frontal area. Furthermore, all those differences gradually decreased with the increase in implantation time. Conclusion The N1 amplitude, N1/P2/MMN latency, and PLI-FC in the alpha band may reflect the process of auditory function remodeling and could be an objective index for the assessment of speech perception ability and the effect of cochlear implantation.