In order to explore the local effects of electrode microstructural inhomogeneity, a half cell Li ion battery was built with reconstructed realistic LiCoO2 cathode electrode which was divided equally into eight subdomains. A previously developed C++ code was used to simulate the discharge and charge processes using finite volume method. The geometric properties of each subdomain were characterized by porosity, tortuosity and specific interfacial area. The average variables, such as Li ion concentration and reaction current density, and polarization due to different sub-processes, such as activation of electrochemical reactions (PAER) and charge transport of species were calculated in each subdomain. The inhomogeneous geometric properties result in non-uniform polarization distribution. The polarization due to ionic transport depends on the position, tortuosity and porosity. The porosity, specific interfacial area, state of discharge/charge and position play an important role in the distribution of PAER. The PAER difference between subdomains tends to enlarge at the end of discharge process but to reduce at the end of charge process although the main electrochemical reaction always takes place in the subdomains with smaller porosity. In addition, the PAER is much larger than the polarization due to ionic transport. By comparing with the results from pseudo 2D model, we found that microstructural inhomogeneity in the 3D model has significant impact on global polarization and polarization distribution in the electrode. The presented method provides a possibility to study local effect of inhomogeneous geometric properties.