Electrochemical impedance spectroscopy (EIS) can provide information about the internal state of fuel cells, which makes EIS an important tool for fuel cell fault diagnosis. However, high cost, large volume, and poor scalability are limitations of existing EIS measurement equipment. In this study, a multi-channel online fuel cell EIS measurement device was designed. In this device, based on multi-phase interleaved Boost topology and average current control, an excitation source, which can output 1~500 Hz, 10 A sinusoidal excitation current was designed and verified by model simulation. Then, based on the quadrature vector digital lock-in amplifier (DLIA) algorithm, an impedance measuring module that can achieve precise online impedance measurement and calculation was designed. A prototype was then built for the experiment. According to the experiment test, the amplitude error of the excitation source is less than 1.8%, and the frequency error is less than 0.3%. Compared with the reference data, the impedance measured by the prototype has a modulus error of less than 3.5% and a phase angle error of less than 1.5°. Moreover, the waveform control and impedance extraction function of the EIS measurement device is implemented on an embedded controller, which can cut the price and reduce the volume.