Objective: To assess the clinical features and the management of skin flap infection (SFI) following cochlear implantation (CI) and to characterize the biofilm features by the scanning electron microscopy.Setting: The study was conducted at a tertiary care center.Participants: A total of 1,251 patients receiving CI in the First Affiliated Hospital of Fujian Medical University between August 2001 and March 2021 were enrolled. Scanning electron microscopy was utilized for characterizing the etiology of infection. Main outcome measures: A proposed stratification system was applied to optimize treatments for post-operation flap infection.Results: After CI, SFI was reported in 16 patients (1.28%) and patients under 18-year-old were more prone to flap infection. Staphylococcus Aureus was found to be the most common bacterial culprit for flap infection, with 6 cases explored in this group (6/16, 37.5%). Bacterial biofilm was observed within the jelly-like substance on the surface of CI equipment of SFI patients. A two-stage stratification was proposed for optimizing the treatment schemes. Conservative therapy was recommended for stage I cases while surgical treatment was the preferred method for stage II patients.Conclusions: Pediatric patients are more susceptible to SFI after CI. The formation of bacterial biofilm may be the vital cause of SFI. The proposed stratification can facilitate the management of SFI.