Because of its high efficiency, low pollution and good stability, proton exchange membrane fuel cell (PEMFC) is considered as one of the most promising technologies for a wide range of applications, such as distributed power generation, transportation, portable power source and automobile. In a PEMFC grid-connected system, the proportion integration (PI) regulator can achieve zero error for the dc components in the rotating frame, but cannot achieve zero error for the ac components in the rotating frame. Hence, the PEMFC grid-connected system will produce a large number of harmonics. In order to overcome this shortcoming, a proportion integration resonant (PIR) controller is utilized to realize zero magnitude error and selective disturbance rejection. Instead of the PIR controller, a vector proportion integration (VPI) controller is designed to quickly and accurately regulate current which achieve zero both amplitude and phase frequency response at the resonant frequency simultaneously. In this paper, the PEMFC grid-connected system based on FIR and VPI controllers are developed according to the operating characteristics of a PEMFC generation system, then analyze and compare the performance of compensation harmonics between them. The total harmonic distortion (THD) of grid-connected voltage and current are measured by means of the criterion of IEEE Std1547-2003. This proposed grid-connected method will provide a novel approach for the design of advanced PEMFC grid-connected control system. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.