The combustion emissions of the hydrogen-fueled engines are very clean, but the problems of abnormal combustion and high NOx emissions limit their applications. Nowadays hydrogen engines use exhaust gas recirculation (EGR) technology to control the intensity of premixed combustion and reduce the NOx emissions. This study aims at improving the abnormal combustion and decreasing the NOx emissions of the hydrogen engine by applying a three-dimensional (3D) computational fluid dynamics (CFD) model of a single-cylinder hydrogen-fueled engine equipped with an EGR system. The results indicated that peak in-cylinder pressure continuously increased with the increase of the ignition advance angle and was closer to the top dead center (TDC). In addition, the mixture was burned violently near the theoretical air−fuel ratio, and the combustion duration was shortened. Moreover, the NOx emissions, the average pressure, and the in-cylinder temperature decreased as the EGR ratio increased. Furthermore, increasing the EGR ratio led to an increase in the combustion duration and a decrease in the peak heat release rate. EGR system could delay the spontaneous combustion reaction of the end-gas and reduce the probability of knocking. The pressure rise rate was controlled and the in-cylinder hot spots were reduced by the EGR system, which could suppress the occurrence of the pre-ignition in the hydrogen engine.