The Roots air compressor has a great potential for air supply in a hydrogen fuel cell vehicle (HFCV) because of its high efficiency, reliable operation, and wide range of flow rates. However, pressure pulsation of the Roots compressor could causes early failure of components of a fuel cell system. In this paper, numerical and experimental investigation on the discharge pressure pulsation of a helical Roots compressor was presented. First, a three-dimensional transient computational fluid dynamics model was built to examine and evaluate the pressure fluctuation amplitude. Then, the influences of angle steps and rotating speed on the fluctuation amplitude of discharge pressure were explored based on the numerical model. Meanwhile, a test rig was carried out to investigate the performance of the air compressor. The maximal discrepancy between experiment and simulation was within 8%. Finally, the effect of the opening angle of the discharge port profile on pressure pulsation was studied. The results showed that the fluctuation amplitude decreased from 6.48% to 1.87% with the opening angle increasing from 77° to 90°. The distribution of velocity showed that the dominating vortexes gradually dissipated with the increase of opening angle, and consequently contributed to the attenuation of the pressure pulsation. It provides new guidance for the structural optimization design of Roots air compressor.