Objectives To investigate the volumetric alterations of hippocampal subfields and identify which subfields contribute to mild cognitive impairment (MCI) in multiple system atrophy (MSA) and Parkinson's disease (PD). Methods Thirty MSA-MCI, 26 PD-MCI, and 30 healthy controls were administered cognitive assessment, along with hippocampal segmentation using FreeSurfer 6.0 after a 3-T MRI scan. Regression analyses were performed between the volumes of hippocampal subfields and cognitive variables. Results Compared with healthy controls, the volume of the hippocampal fissure was enlarged in PD-MCI patients, while left Cornu Ammonis (CA2-CA3), bilateral molecular layer, bilateral hippocampus-amygdala transition area, right subiculum, right CA1, right presubiculum, right parasubiculum, and bilateral whole hippocampus were reduced in the MSA-MCI group. Moreover, volumetric reductions of the bilateral hippocampal tail, bilateral CA1, bilateral presubiculum, bilateral molecular layer, left CA2-CA3, left hippocampus-amygdala transition area, right parasubiculum, and bilateral whole hippocampus were found in MSA-MCI relative to the PD-MCI group. The volumes of the left CA2-CA3 (B = - 11.34, p = 0.006) and left parasubiculum (B = 4.63, p = 0.01) were respectively correlated with language and abstraction functions. The volumes of the left fimbria (B = 6.99, p = 0.002) and left hippocampus-amygdala transition area (B = 2.28, p = 0.009) were correlated with visuospatial/executive function. Conclusions The MSA-MCI patients showed more widespread impairment of hippocampal subfields compared with the PD-MCI group, involving trisynaptic loop and amygdala-hippocampus interactions. The alteration of CA, hippocampus-amygdala transition area, and fimbria still requires further comparison between the two patient groups.