Proton exchange membrane fuel cell (PEMFC) system is expected to be the next generation vehicle powertrain. However, water management is still the main problem which directly affects the performance, reliability and durability in PEMFC system. To ensure the accurate water content estimation, High Frequency Resistance (HFR) is the most representative indicator in laboratory. The HFR is calculated by detecting the Alternating Current (AC) voltage response of fuel cell under the excitation of 1k Hz AC current. The voltage level of the AC excitation affects the measurement of HFR. Generally, 5mV AC excitation is used to measure HFR for the fuel cell with an output voltage between 0.6-1V. So, online HFR monitor is a big challenge for vehicle application, due to its low Signal/Noise Ratio (S/N), poor Electromagnetic Compatibility (EMC) environment, high common mode voltage and several hundred cells. In this work, an online fuel cell HFR monitor controller is developed. Firstly, in order to amplify the weak AC voltage signal, the high voltage and high precision operational amplifier and active filter are used. High precision Analog-to-Digital Convertor (ADC) and high speed processor are used to process the signal. The measuring circuit can withstand a 600V common-mode voltage and simultaneously measure 16 pieces of fuel cell. It can meet the acquirements of 60kW PEMFC system. In HFR calculation, both the Fast Fourier Transformation (FFT) and amplitude ratio measurement chip are used to check the results. Finally, the controller is tested in the test bench. The results prove that the software and hardware design is feasible and the function is basically normal in real time.