Objective The aim of this study was to examine the change in the hippocampal volume and shape in early-onset mild cognitive impairment(EO-MCI) associated with the APOE ε4 carrier state. Methods This study had 50 subjects aged 55–63 years, all of whom were diagnosed with MCI at baseline via the Korean version of the Consortium to Establish a Registry for Alzheimer’s Disease Assessment Packet. The EO-MCI patients were divided into the MCI continued (MCIcont) and Alzheimer’s disease (AD) converted (ADconv) groups 2 years later. The hippocampal volume and shape were measured for all the subjects. The local shape analysis (LSA) was used to conduct based on the 2-year-interval magnetic resonance imaging scans. Results There was a significant correlation between APOE ε4 allele and hippocampal volume atrophy. Over two years, the volume reduction in the left hippocampus was found to be faster than that in the right hippocampus, especially in the APOE ε4 carriers. LSA showed that the 2 subfields were significantly affected in the left hippocampus. Conclusion These results suggest that the possession of APOE ε4 allele may lead to greater predilection for left hippocampal atrophy in EO-MCI, and some specific subfields of the hippocampus may be more prominently involved.