Concerning the adverse environmental impacts of fossil fuel consumption, many investigations have been performed on choosing more environmentally friendly fuel alternatives and sustainable resources. In this regard, hydrogen is considered to be one of the promising alternative fuels as its combustion features are the most similar to fossil fuels and it also falls into the category of renewable and clean fuels. This article studies the simulation of hydrogen-diesel combustion in heavy duty engine at full load and speed of 1600 rpm. All engine features including speed, spray angle, spray duration and input power are held fixed in the simulation. Variable parameter is the ratio of mass or hydrogen energy to diesel. Depending on input power of diesel, hydrogen is changed from 0% (pure diesel) to 70% (i.e. 70% is supplied from the input power of hydrogen and the remaining 30% from diesel fuel). The results of simulation show that hydrogen substitution with diesel at the best state leads to reduction of pollutants such as nitric oxides, carbon dioxide, unburned hydrocarbon, soot and carbon monoxide to 8%, 14%, 54%, 14% and 70%, respectively. This substitution however causes the reduction of indicated efficiency to 2.8%. Hydrogen substitution with diesel can also postpone the combustion, and resulting to increase PRR and HRR; however, this pressure enhancement does not lead to knocking.