LiCoO2/mesocarbon microbeads (MCMB) batteries are over-charged to different voltage (4.4 V, 4.5 V, 4.6 V, and 4.7 V, respectively) for ten times, and then are cycled 1000 times for shallow depth of discharge. The morphology, structure, and electrochemical performance of the electrode materials were studied in detail in order to identify the capacity fading mechanism of over-charged battery after long-term cycling. The cycling performances of LiCoO2/MCMB batteries are gradually aggravated with the increase of over-charging voltage and the degradation mechanism is diverse upon the degree of over-charging. The capacity fading after long-term cycling of battery over-charged to 4.6 V or 4.7 V is mainly attributed to the cathodes. Soft X-ray absorption spectroscopy (XAS) demonstrates that the lower valence state of cobalt exists on the surface of the LiCoO2 after serious over-charging (4.6 V or 4.7 V), and cobalt is dissolved then deposited on the anode according to the result of energy dispersive spectrometry (EDS). However, after shallow over-charging (4.4 V or 4.5 V), the capacity deterioration is proposed as the loss of active lithium, presented by the generation of the SEI film on the anode, which is verified by water washed tests.