The active lithium loss in cathode materials is responsible for the capacity fading of LiFePO4/graphite battery at ambient temperature and low C-rate. In this work, we investigate the changes of lithium amount in four components involving cathode, anode, separator and electrolyte at different capacity loss levels when the LiFePO4/graphite batteries are cycled at a rate of 2C. The results show that the lithium content in the cathode decreases from 4.2% to 1.8% as the capacity retention decreases to 23.4%, while that in the graphite anode increases from 1.1% to 4.9%. Internal and intrinsic fading causes are investigated by subsequent analysis of their structures and morphologies. Besides, electrochemical testing results show that the loss of lithium ions for the cycled LiFePO4 electrodes is restorable due to the well-maintained olivine structure, while the cycled graphite anodes exhibit quick fading of charging/discharging specific capacity after long-term cycling. The capacity fading mechanism can be mainly ascribed to the active lithium consumption on graphite anode for solid electrolyte interface breaking/repairing and side reactions induced by graphite's inner structural deterioration.