Commercial LiCoO2/mesocarbon microbeads (MCMB) batteries (CP475148AR) are short circuited by different contact resistances (0.6 mΩ and 5.0 mΩ) for short times. The short circuited battery is cycled for 1000 times, and the effect of the short-time external short circuiting on the capacity fading mechanism during long-term cycling of LiCoO2/MCMB battery is studied by analyzing the morphology, structure, and electrochemical performance. The results of SEM indicates that the morphology of LiCoO2 material is almost unchanged, except that the particle surface becomes smooth, and the solid electrolyte interphase (SEI) film on the surface of MCMB electrode becomes nonuniform due to the high temperature caused by short circuiting. The lithium ions are more difficult to de-intercalate from the anode and the lattice structure of LiCoO2 degrades according to the results of X-ray diffraction (XRD). The high discharge current caused by short circuiting can damage electrodes, leaving vacancies in structure. The damage of electrode structure can lead to a decrease of diffusion coefficient of lithium (D), so polarization increases and mainly caused by the LiCoO2 electrode. The capacity deterioration of short circuited battery during long-term cycling is mainly caused by the increase of polarization and capacity loss of electrodes.