Although an inverse-spinel MnCo2O4 has been widely used as a promising supercapacitor material due to its high theoretical capacitance (>3000 F g−1), the supercapacitor device of MnCo2O4 exhibits poor capacity retention, only 79% after 2500 cycles, limiting its practical application. In situ electrochemical X-ray absorption spectroscopy (XAS), in situ mass detection electrochemical quartz crystal microbalance (EQCM), ex situ field emission scanning electron microscopy (FESEM), and ex situ extended X-ray absorption fine structure (EXAFS) were used to investigate charge storage mechanism of the MnCo2O4 and the origin of its capacity retention fading. It was found that the capacity retention of MnCo2O4 supercapacitors is sensitive to the concentration of electrolyte. High concentration (e.g., 6 M) of KOH electrolyte provides poor capacity retention due to the Jahn-Teller distortion at the positive electrode and the phase transformation at the negative electrode. More interestingly, the MnCo2O4 used at the negative electrode is less stable than that used at the positive electrode. Using low concentration of KOH (i.e., 1 M) and the asymmetric supercapacitor design using MnCo2O4 at the positive electrode would enhance their charge storage performance with high capacity retention.