In the process of fuel oxidation, various harmful substances are formed in the compression ignition engine (CIE) cylinder, including nitrogen compounds and soot. The presence of these components, and especially soot, has a decisive role in the processes of thermal radiation of the flame, local heat transfer in the CC, the degree of blackness of the flame, the thermal stress of the piston and cylinder cover. Under the conditions of non-stationary processes, it is necessary to solve local problems by determining the concentration of these substances, taking into account the uneven distribution of fuel, the non-stationary local thermal conditions and the various state of aggregation of the components of the medium. The presence of soot leads to the formation of soot, which leads to disruption of heat transfer processes between the functioning fluid and the cylinder cover and the piston bottom, that is, the conditions in the boundary layer. The concentrations of these substances depending on the operating parameters of the CIE are considered, recommendations are made on the practical use of compressed natural gas in a tractor CIE.