Adding hydrogen to natural gas is a promising way to improve the ignition stability and reduce the greenhouse gas emissions of pilot-ignition direct-injection natural gas engines. Most of the previous studies concerning hydrogen-enriched natural gas engines are focused on spark-ignition engines. The limited investigations on the addition of hydrogen in direct-injection natural gas engines are conducted by experimental method. Therefore, some detailed information on the in-cylinder combustion and emission formation process are left unknown. In this work, numerical simulations have been performed for the combustion process of a pilot-ignition direct-injection natural gas engine based on an integrated mechanism which is capable of describing the chemical kinetics involving diesel, natural gas, and hydrogen. Three-dimensional (3D) computational fluid dynamics simulations were conducted at different hydrogen blend ratios to explore the effects of hydrogen addition on the whole combustion process and the mole fraction traces of small radicals as well as CO, NOx, and soot emissions. Hydrogen addition was achieved by both volume-equivalent principle and energy-equivalent principle to guide the choice of hydrogen-addition method. Zero-dimensional simulations were conducted to elaborate the explanations of the phenomena in 3D simulations and disclose the interactions among the sensitivity of the key reactions, the formation of the active radicals, and the heat release process. The results show that the ignition delay is shortened and the ignition of natural gas is enhanced with the increase of hydrogen addition, which is primarily caused by the enhanced reactions related to active small radicals induced by increased hydrogen concentration. When hydrogen is added based on the volume-equivalent principle, all emission values will reduce with little sacrifice on thermal efficiency at hydrogen blend ratios smaller than 20%. However, CO emissions experience an increasing trend when hydrogen blend ratio is further increased to higher than 20% while NOx and soot emissions retain the decreasing trend. When hydrogen is added based on the energy-equivalent principle, CO emissions and soot emissions will decrease with the increase of hydrogen blend ratio while NOx emissions will witness an opposite trend with considerable improvements in thermal efficiency.