MCMBs with different crystal structure were tested for an anode of lithium ion batteries (LIB) and the model describing the behavior of porous anodes was simulated numerically by using orthogonal collocation method (OCM). Kinetic parameters such as diffusion coefficients, exchange current densities, and transfer coefficient, describing electrochemical intercalation system of lithium ions, were estimated by fitting the experimental cyclic voltametry (CV) results with the theoretical ones. It was investigated that the theoretical cyclic voltamograms obtained using above parameters fitted well with the experimental curves for the various scan rates from 1 mV s−1 to 5 μV s−1. The parameters were then evaluated on their extended application in various C-rate-charge/discharge cycling tests with showing good agreements between experiments and simulations. As the results show, it was found that numerical simulations based on both potentiometry and galvanometry experimental data resulted in more accurate parameters of electrochemical system. Simulations indicate there exist the optimum design conditions of electrode and separator to obtain the good performance of lithium ion batteries.