In electric vehicles (EVs), several battery cells are connected in parallel to establish a battery module. The safety of the battery module is influenced by inconsistent battery cell performance which causes uneven currents flowing through internal in-parallel battery cells. A battery cell model is developed based on the Matlab–Simscape platform and validated by tests. The battery cell model is used to construct simulation models for analyzing the effect of battery cell inconsistency on the performance of an in-parallel battery module. Simulation results indicate that the state-of-charge (SOC) of a battery module cannot characterize the SOC of ALL the internal battery cells in the battery module. When the battery management system (BMS) controls the end-of-charge (EOC) time according to the SOC of a battery module, some internal battery cells are over-charged. To guarantee the safety of ALL battery cells through the whole battery life, a safety EOC voltage of the battery module should be set according to the number of battery cells in the battery module and the applied charge current. Simulations reveal that the SOC of the “normal battery module” is related to its charge voltage when aged battery module is charged to the EOC voltage. Then, a function describing their relationship is established. Both the capacity and the charge voltage shift are estimated by comparing the measured voltage-to-capacity curve with the standard one provided by the manufactory. A battery pack capacity estimation method is proposed according to the SOC and the capacity of the “normal battery module”. Experimental results show that battery pack capacity estimation difference between the proposed method and the standard current integration method is to within 0.35%.