A series of Li-ion cells with a LiCoO2 cathode, artificial graphite anode and a LiPF6-based nonaqueous electrolyte were stored at 55°C in a series of state of charge (SoC) from 0 to 100%. After storage, all the cells except the one stored in 0% SoC exhibited capacity fade and cycling performance decline, which were aggravated by increasing storage SoC. Furthermore, storage at higher SoC increased the safety risk of the cells. The cells stored at SoC higher than 50% could not pass the 3C/5V overcharge test, while such a test was easy to pass for the fresh cells and those stored at 0% SoC. The above results show that the fully discharged state is a favorable storage condition to maintain good storage performance of Li-ion cells. In addition, to clarify the aging mechanisms of the cells, XRD (X-ray diffraction), SEM (scanning electron microscopy) and EIS (electrochemical impedance spectra) measurements were carried out. The results indicate that the performance fading of the stored cells is not due to the bulk structure change of the electrode materials, but instead due to the microstructure variation of the cathode, including the decrease in the crystallite dimension, the change of the micro-stress, and the precipitation of the surface films over the electrodes. According to EIS analysis, the increase of the cathode impedance may be the main contributor to the overall degradation of the Li-ion cells after storage.