The aging mechanisms of Nickel-Manganese-Cobalt-Oxide (NMC)/Graphite lithium-ion batteries are divided into stages from the beginning-of-life (BOL) to the end-of-life (EOL) of the battery. The corresponding changes in the battery performance across these stages have been analyzed, and a digital twin model is established to quantify the primary parameters that influence these aging mechanisms. Post-mortem analysis is applied to validate the results. This paper compares the aging mechanisms from BOL to EOL using two charging protocols: a multi-step fast charge protocol and a common constant-current fast charge protocol that applies the average current of multi-step currents. Notably, a transition from a linear to a non-linear degradation trend in capacity fade is observed, beginning from a 10% capacity reduction to EOL. From BOL to 10% degradation, the resistance of solid electrolyte interphase (SEI) grows steadily. The graphite anode’s crack depth exhibits a significant increase, accompanied by an evident collapse of cathode materials in all the test cases following a 10% degradation until EOL. This phenomenon can be attributed to one primary reason—the expansion of the corresponding simulated resistance of charge transfer (Rct). Post-mortem analysis revealed the change in morphology, structure, and composition of various degradation conditions. This analysis proved that the primary driver of the linear aging stage is the SEI growth. Furthermore, it is evident that the transition to a non-linear aging degradation is dominated by electrode defects resulting from continuous mechanical stress during long-term aging.