As the dependence on fossil fuel increases in the transportation sector, more attention has been paid to the energy management control of proton exchange membrane fuel cell (PEMFC) plug-in hybrid electric vehicles (PHEVs). In this paper, the energy management control problem for a series plug-in PEMFC/Li-ion battery hybrid midsize sedan is formulated and investigated using a two-stage controller (TSC). The control objective is to minimize hydrogen consumption and simultaneously protect PEMFC health. The proposed TSC consists of two controllers designed in two stages with different control functions. During the first design stage, a predictive controller is developed using the telemetry equivalent consumption minimization strategy (T-ECMS) approach to predict the global battery state-of-charge (SOC) optimality trend and local control reference, without regard for the PEMFC health constraints. During the second stage of design, a tracking controller is designed to track the local control reference with respect to the PEMFC health constraints and other physical limitations at the current control step, which ensures that the system follows the optimal battery SOC reference over a long time horizon. Finally, the effectiveness of the proposed TSC is compared with the T-ECMS and an electric vehicle controller (EVC) under the Matlab/Simulink software environment. The results demonstrate that the TSC achieves a reasonable tradeoff between hydrogen fuel consumption and PEMFC health protection.